From 061706a4a41ee6421c1229a48908009eb0d34fa0 Mon Sep 17 00:00:00 2001
From: d-callan <53306535+d-callan@users.noreply.github.com>
Date: Thu, 30 May 2024 14:33:30 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20microbio?=
 =?UTF-8?q?meDB/microbiomeData@ab2ad9cbe165b780b56b67a838d1233cc3152e3a=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                               | 2 +-
 LICENSE.html                           | 2 +-
 authors.html                           | 6 +++---
 index.html                             | 2 +-
 pkgdown.yml                            | 2 +-
 reference/Anopheles_albimanus.html     | 2 +-
 reference/BONUS.html                   | 2 +-
 reference/Bangladesh.html              | 2 +-
 reference/DailyBaby.html               | 2 +-
 reference/DiabImmune.html              | 2 +-
 reference/ECAM.html                    | 2 +-
 reference/EcoCF.html                   | 2 +-
 reference/FARMM.html                   | 2 +-
 reference/GEMS1.html                   | 2 +-
 reference/HMP_MGX.html                 | 2 +-
 reference/HMP_V1V3.html                | 2 +-
 reference/HMP_V3V5.html                | 2 +-
 reference/Leishmaniasis.html           | 2 +-
 reference/MALED_2yr.html               | 2 +-
 reference/MALED_diarrhea.html          | 2 +-
 reference/MORDOR.html                  | 2 +-
 reference/Malaysia_helminth.html       | 2 +-
 reference/NICU_NEC.html                | 2 +-
 reference/PIH_Uganda.html              | 2 +-
 reference/PretermInfantResistome1.html | 2 +-
 reference/PretermInfantResistome2.html | 2 +-
 reference/UgandaMaternal.html          | 2 +-
 reference/getCuratedDatasetNames.html  | 2 +-
 reference/index.html                   | 2 +-
 reference/microbiomeData-package.html  | 2 +-
 search.json                            | 2 +-
 31 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/404.html b/404.html
index e711ba3..0eede7a 100644
--- a/404.html
+++ b/404.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="https://microbiomedb.github.io/microbiomeData/index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE.html b/LICENSE.html
index 13c2aa7..69b72aa 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/authors.html b/authors.html
index 7e179fd..fae6be3 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -55,13 +55,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Callan D (2024).
 <em>microbiomeData: Curated Data from MicrobiomeDB.org</em>.
-R package version 1.0.3, https://microbiomedb.github.io/microbiomeData/, <a href="https://github.com/microbiomeDB/microbiomeData" class="external-link">https://github.com/microbiomeDB/microbiomeData</a>. 
+R package version 1.0.4, https://microbiomedb.github.io/microbiomeData/, <a href="https://github.com/microbiomeDB/microbiomeData" class="external-link">https://github.com/microbiomeDB/microbiomeData</a>. 
 </p>
       <pre>@Manual{,
   title = {microbiomeData: Curated Data from MicrobiomeDB.org},
   author = {Danielle Callan},
   year = {2024},
-  note = {R package version 1.0.3, https://microbiomedb.github.io/microbiomeData/},
+  note = {R package version 1.0.4, https://microbiomedb.github.io/microbiomeData/},
   url = {https://github.com/microbiomeDB/microbiomeData},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index 9a9b5dc..4592999 100644
--- a/index.html
+++ b/index.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/pkgdown.yml b/pkgdown.yml
index 904d0b7..b1db5da 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 3.1.11
 pkgdown: 2.0.9
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-05-29T15:36Z
+last_built: 2024-05-30T14:33Z
 urls:
   reference: https://microbiomedb.github.io/microbiomeData/reference
   article: https://microbiomedb.github.io/microbiomeData/articles
diff --git a/reference/Anopheles_albimanus.html b/reference/Anopheles_albimanus.html
index 60f2e33..e9d5cf8 100644
--- a/reference/Anopheles_albimanus.html
+++ b/reference/Anopheles_albimanus.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/BONUS.html b/reference/BONUS.html
index 9a9b578..a34c1d2 100644
--- a/reference/BONUS.html
+++ b/reference/BONUS.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/Bangladesh.html b/reference/Bangladesh.html
index f780534..1f39dee 100644
--- a/reference/Bangladesh.html
+++ b/reference/Bangladesh.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/DailyBaby.html b/reference/DailyBaby.html
index ddd70e4..7e28de1 100644
--- a/reference/DailyBaby.html
+++ b/reference/DailyBaby.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/DiabImmune.html b/reference/DiabImmune.html
index ba45986..bb6a72b 100644
--- a/reference/DiabImmune.html
+++ b/reference/DiabImmune.html
@@ -22,7 +22,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/ECAM.html b/reference/ECAM.html
index bab6659..b4e6082 100644
--- a/reference/ECAM.html
+++ b/reference/ECAM.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/EcoCF.html b/reference/EcoCF.html
index eebb53a..6530a6c 100644
--- a/reference/EcoCF.html
+++ b/reference/EcoCF.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/FARMM.html b/reference/FARMM.html
index 9820e3d..0dc28f9 100644
--- a/reference/FARMM.html
+++ b/reference/FARMM.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/GEMS1.html b/reference/GEMS1.html
index 1bce39d..47c45c3 100644
--- a/reference/GEMS1.html
+++ b/reference/GEMS1.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/HMP_MGX.html b/reference/HMP_MGX.html
index 992988e..e224577 100644
--- a/reference/HMP_MGX.html
+++ b/reference/HMP_MGX.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/HMP_V1V3.html b/reference/HMP_V1V3.html
index 82d793f..c893a35 100644
--- a/reference/HMP_V1V3.html
+++ b/reference/HMP_V1V3.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/HMP_V3V5.html b/reference/HMP_V3V5.html
index ce1d65f..20ba743 100644
--- a/reference/HMP_V3V5.html
+++ b/reference/HMP_V3V5.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/Leishmaniasis.html b/reference/Leishmaniasis.html
index c12e816..9bcf0f0 100644
--- a/reference/Leishmaniasis.html
+++ b/reference/Leishmaniasis.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/MALED_2yr.html b/reference/MALED_2yr.html
index 01cb54a..4a10919 100644
--- a/reference/MALED_2yr.html
+++ b/reference/MALED_2yr.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/MALED_diarrhea.html b/reference/MALED_diarrhea.html
index 837e96f..38d719a 100644
--- a/reference/MALED_diarrhea.html
+++ b/reference/MALED_diarrhea.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/MORDOR.html b/reference/MORDOR.html
index 2c1b130..3e67349 100644
--- a/reference/MORDOR.html
+++ b/reference/MORDOR.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/Malaysia_helminth.html b/reference/Malaysia_helminth.html
index 1703cf1..360dda6 100644
--- a/reference/Malaysia_helminth.html
+++ b/reference/Malaysia_helminth.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/NICU_NEC.html b/reference/NICU_NEC.html
index 2a4111e..9217f59 100644
--- a/reference/NICU_NEC.html
+++ b/reference/NICU_NEC.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/PIH_Uganda.html b/reference/PIH_Uganda.html
index c4e32c3..c35fa56 100644
--- a/reference/PIH_Uganda.html
+++ b/reference/PIH_Uganda.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/PretermInfantResistome1.html b/reference/PretermInfantResistome1.html
index 3228ef3..5524ff0 100644
--- a/reference/PretermInfantResistome1.html
+++ b/reference/PretermInfantResistome1.html
@@ -22,7 +22,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/PretermInfantResistome2.html b/reference/PretermInfantResistome2.html
index 28a648e..944c467 100644
--- a/reference/PretermInfantResistome2.html
+++ b/reference/PretermInfantResistome2.html
@@ -22,7 +22,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/UgandaMaternal.html b/reference/UgandaMaternal.html
index ea6d968..873b48b 100644
--- a/reference/UgandaMaternal.html
+++ b/reference/UgandaMaternal.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getCuratedDatasetNames.html b/reference/getCuratedDatasetNames.html
index 0fef807..c99c22a 100644
--- a/reference/getCuratedDatasetNames.html
+++ b/reference/getCuratedDatasetNames.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index 10d0dbd..61536a6 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
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diff --git a/reference/microbiomeData-package.html b/reference/microbiomeData-package.html
index f94297e..7df8ff7 100644
--- a/reference/microbiomeData-package.html
+++ b/reference/microbiomeData-package.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
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diff --git a/search.json b/search.json
index 767fa9a..3ff8344 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://microbiomedb.github.io/microbiomeData/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"Apache License","title":"Apache License","text":"Version 2.0, January 2004 <http://www.apache.org/licenses/>","code":""},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/LICENSE.html","id":"id_1-definitions","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"1. Definitions","title":"Apache License","text":"“License” shall mean terms conditions use, reproduction, distribution defined Sections 1 9 document. “Licensor” shall mean copyright owner entity authorized copyright owner granting License. “Legal Entity” shall mean union acting entity entities control, controlled , common control entity. purposes definition, “control” means () power, direct indirect, cause direction management entity, whether contract otherwise, (ii) ownership fifty percent (50%) outstanding shares, (iii) beneficial ownership entity. “” (“”) shall mean individual Legal Entity exercising permissions granted License. “Source” form shall mean preferred form making modifications, including limited software source code, documentation source, configuration files. “Object” form shall mean form resulting mechanical transformation translation Source form, including limited compiled object code, generated documentation, conversions media types. “Work” shall mean work authorship, whether Source Object form, made available License, indicated copyright notice included attached work (example provided Appendix ). “Derivative Works” shall mean work, whether Source Object form, based (derived ) Work editorial revisions, annotations, elaborations, modifications represent, whole, original work authorship. purposes License, Derivative Works shall include works remain separable , merely link (bind name) interfaces , Work Derivative Works thereof. “Contribution” shall mean work authorship, including original version Work modifications additions Work Derivative Works thereof, intentionally submitted Licensor inclusion Work copyright owner individual Legal Entity authorized submit behalf copyright owner. purposes definition, “submitted” means form electronic, verbal, written communication sent Licensor representatives, including limited communication electronic mailing lists, source code control systems, issue tracking systems managed , behalf , Licensor purpose discussing improving Work, excluding communication conspicuously marked otherwise designated writing copyright owner “Contribution.” “Contributor” shall mean Licensor individual Legal Entity behalf Contribution received Licensor subsequently incorporated within Work.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/LICENSE.html","id":"id_2-grant-of-copyright-license","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"2. 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Submission of Contributions","title":"Apache License","text":"Unless explicitly state otherwise, Contribution intentionally submitted inclusion Work Licensor shall terms conditions License, without additional terms conditions. Notwithstanding , nothing herein shall supersede modify terms separate license agreement may executed Licensor regarding Contributions.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/LICENSE.html","id":"id_6-trademarks","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"6. 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Disclaimer of Warranty","title":"Apache License","text":"Unless required applicable law agreed writing, Licensor provides Work (Contributor provides Contributions) “” BASIS, WITHOUT WARRANTIES CONDITIONS KIND, either express implied, including, without limitation, warranties conditions TITLE, NON-INFRINGEMENT, MERCHANTABILITY, FITNESS PARTICULAR PURPOSE. solely responsible determining appropriateness using redistributing Work assume risks associated exercise permissions License.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/LICENSE.html","id":"id_8-limitation-of-liability","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"8. Limitation of Liability","title":"Apache License","text":"event legal theory, whether tort (including negligence), contract, otherwise, unless required applicable law (deliberate grossly negligent acts) agreed writing, shall Contributor liable damages, including direct, indirect, special, incidental, consequential damages character arising result License use inability use Work (including limited damages loss goodwill, work stoppage, computer failure malfunction, commercial damages losses), even Contributor advised possibility damages.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/LICENSE.html","id":"id_9-accepting-warranty-or-additional-liability","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"9. Accepting Warranty or Additional Liability","title":"Apache License","text":"redistributing Work Derivative Works thereof, may choose offer, charge fee , acceptance support, warranty, indemnity, liability obligations /rights consistent License. However, accepting obligations, may act behalf sole responsibility, behalf Contributor, agree indemnify, defend, hold Contributor harmless liability incurred , claims asserted , Contributor reason accepting warranty additional liability. END TERMS CONDITIONS","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/LICENSE.html","id":"appendix-how-to-apply-the-apache-license-to-your-work","dir":"","previous_headings":"","what":"APPENDIX: How to apply the Apache License to your work","title":"Apache License","text":"apply Apache License work, attach following boilerplate notice, fields enclosed brackets [] replaced identifying information. (Don’t include brackets!) text enclosed appropriate comment syntax file format. also recommend file class name description purpose included “printed page” copyright notice easier identification within third-party archives.","code":"Copyright [yyyy] [name of copyright owner]  Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at    http://www.apache.org/licenses/LICENSE-2.0  Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License."},{"path":"https://microbiomedb.github.io/microbiomeData/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Danielle Callan. Author, maintainer.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Callan D (2024). microbiomeData: Curated Data MicrobiomeDB.org. R package version 1.0.3, https://microbiomedb.github.io/microbiomeData/, https://github.com/microbiomeDB/microbiomeData.","code":"@Manual{,   title = {microbiomeData: Curated Data from MicrobiomeDB.org},   author = {Danielle Callan},   year = {2024},   note = {R package version 1.0.3, https://microbiomedb.github.io/microbiomeData/},   url = {https://github.com/microbiomeDB/microbiomeData}, }"},{"path":"https://microbiomedb.github.io/microbiomeData/index.html","id":"microbiomedata","dir":"","previous_headings":"","what":"Curated Data from MicrobiomeDB.org","title":"Curated Data from MicrobiomeDB.org","text":"R package containing curated datasets MicrobiomeDB.org helper function list datasets available.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Curated Data from MicrobiomeDB.org","text":"Use R package remotes install microbiomeData. R command prompt:","code":"remotes::install_github('microbiomeDB/microbiomeData')"},{"path":"https://microbiomedb.github.io/microbiomeData/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Curated Data from MicrobiomeDB.org","text":"package contains curated datasets MicrobiomeDB.org. extension MicrobiomeDB R package can used analyze visualize data. package installed attached one.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/index.html","id":"direct-usage","dir":"","previous_headings":"Usage","what":"Direct Usage","title":"Curated Data from MicrobiomeDB.org","text":"can get list curated datasets available within package following: favorite dataset myData, can ask specific collections dataset. collection group variables represent biologically coherent concept measured comparable range. Relative abundances specific taxonomic rank example. might look something like:","code":"microbiomeData::getCuratedDatsetNames() myData <- microbiomeData::DiabImmune getCollectionNames(myData) # will print the names of collections myCollection <- getCollection(myData, '16S (V4) Species')"},{"path":"https://microbiomedb.github.io/microbiomeData/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Curated Data from MicrobiomeDB.org","text":"Apache 2.0","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Anopheles_albimanus.html","id":null,"dir":"Reference","previous_headings":"","what":"Anopheles albimanus — Anopheles_albimanus","title":"Anopheles albimanus — Anopheles_albimanus","text":"study assessed impact pyrethroid exposure internal cuticle microbiome Anopheles albimanusi. 125 samples, pool 3 mosquitos. V3-V4 region 16S rRNA gene. Adult larval Anopheles albimanus collected around Las Cruces, Guatemala.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Anopheles_albimanus.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Anopheles albimanus — Anopheles_albimanus","text":"","code":"Anopheles_albimanus"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Anopheles_albimanus.html","id":"anopheles-albimanus","dir":"Reference","previous_headings":"","what":"Anopheles_albimanus","title":"Anopheles albimanus — Anopheles_albimanus","text":"MbioDataset object 12 metadata variables, 125 16S samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Anopheles_albimanus.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Anopheles albimanus — Anopheles_albimanus","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_36cb9bab56/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Anopheles_albimanus.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Anopheles albimanus — Anopheles_albimanus","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/BONUS.html","id":null,"dir":"Reference","previous_headings":"","what":"BONUS-CF — BONUS","title":"BONUS-CF — BONUS","text":"Baby Observational Nutrition Study (BONUS) set identify microbial correlates poor growth observed infants cystic fibrosis (CF) 207 infants diagnosed cystic fibrosis newborn screening Shotgun metagenomic sequencing 122 samples collected healthy controls, 1157 stool samples infants CF collected months 3, 4, 5, 6, 8, 10 12 life Longitudinal, observational, multicenter cohort study.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/BONUS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"BONUS-CF — BONUS","text":"","code":"BONUS"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/BONUS.html","id":"bonus","dir":"Reference","previous_headings":"","what":"BONUS","title":"BONUS-CF — BONUS","text":"MbioDataset object 23 metadata variables, 1279 shotgun metagenomic stool samples. contains following collections:  \"Shotgun metagenomics: 4th level EC metagenome abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway coverage data\"   \"Shotgun metagenomics: Genus\"  \"Shotgun metagenomics: Species\"  \"Shotgun metagenomics: Family\"  \"Shotgun metagenomics: Order\"  \"Shotgun metagenomics: Phylum\"  \"Shotgun metagenomics: Class\"   \"Shotgun metagenomics: Kingdom\"   \"Shotgun metagenomics: Normalized number taxon-specific sequence matches\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/BONUS.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"BONUS-CF — BONUS","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_b3b3ae9838/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/BONUS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"BONUS-CF — BONUS","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Bangladesh.html","id":null,"dir":"Reference","previous_headings":"","what":"Bangladesh 5yr — Bangladesh","title":"Bangladesh 5yr — Bangladesh","text":"study set define normal maturation gut microbiome first 5 years postnatal life. 55 members birth cohort consistently healthy anthropometric scores living within Mirpur district Dhaka, Bangladesh. 2415 stool samples; V4 region 16S rRNA gene. Prospective cohort design monthly sampling first ~5 years life.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Bangladesh.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bangladesh 5yr — Bangladesh","text":"","code":"Bangladesh"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Bangladesh.html","id":"bangladesh","dir":"Reference","previous_headings":"","what":"Bangladesh","title":"Bangladesh 5yr — Bangladesh","text":"MbioDataset object 14 metadata variables, 2145 16S stool samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Bangladesh.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Bangladesh 5yr — Bangladesh","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_1102462e80/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Bangladesh.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Bangladesh 5yr — Bangladesh","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/DailyBaby.html","id":null,"dir":"Reference","previous_headings":"","what":"DailyBaby — DailyBaby","title":"DailyBaby — DailyBaby","text":"Near daily fecal specimens collected term infants first year life. 12 healthy term infants born Oslo, Norway. 2684 stool samples total, average 224 samples (range 116–267) per infant. Prospective cohort design.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/DailyBaby.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DailyBaby — DailyBaby","text":"","code":"DailyBaby"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/DailyBaby.html","id":"dailybaby","dir":"Reference","previous_headings":"","what":"DailyBaby","title":"DailyBaby — DailyBaby","text":"MbioDataset object 17 metadata variables, 2684 16S stool samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/DailyBaby.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"DailyBaby — DailyBaby","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_5a4f8a1791/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/DailyBaby.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"DailyBaby — DailyBaby","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/DiabImmune.html","id":null,"dir":"Reference","previous_headings":"","what":"DiabImmune — DiabImmune","title":"DiabImmune — DiabImmune","text":"Broad Institute's study three pediatric cohorts examined microbiome children high risk development Type 1 diabetes (T1D). Includes 289 children across three sites, including Russia (Karelia), Finland Estonia. 3184 stool samples amplicon sequencing data V4 region 16S rRNA gene. 1149 stool samples 'shotgun' metagenomic sequencing data. Prospective cohort design monthly sampling first ~3 years life. Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/DiabImmune.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DiabImmune — DiabImmune","text":"","code":"DiabImmune"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/DiabImmune.html","id":"diabimmune","dir":"Reference","previous_headings":"","what":"DiabImmune","title":"DiabImmune — DiabImmune","text":"MbioDataset object 60 metadata variables, 3184 16S stool samples 1149 shotgun stool samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"  \"Shotgun metagenomics: 4th level EC metagenome abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway coverage data\"   \"Shotgun metagenomics: Genus\"  \"Shotgun metagenomics: Species\"  \"Shotgun metagenomics: Family\"  \"Shotgun metagenomics: Order\"  \"Shotgun metagenomics: Phylum\"  \"Shotgun metagenomics: Class\"   \"Shotgun metagenomics: Kingdom\"   \"Shotgun metagenomics: Normalized number taxon-specific sequence matches\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/DiabImmune.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"DiabImmune — DiabImmune","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_a2f8877e68/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/ECAM.html","id":null,"dir":"Reference","previous_headings":"","what":"ECAM — ECAM","title":"ECAM — ECAM","text":"Early Childhood Antibiotics Microbiome (ECAM) study set identify impact antibiotics, delivery mode diet infant gut Microbiome. Prospective cohort design healthy humans USA. 43 infants sampled first two years life. 1216 samples various types; V4 region 16S rRNA gene.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/ECAM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ECAM — ECAM","text":"","code":"ECAM"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/ECAM.html","id":"ecam","dir":"Reference","previous_headings":"","what":"ECAM","title":"ECAM — ECAM","text":"MbioDataset object 27 metadata variables, 1216 16S samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/ECAM.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"ECAM — ECAM","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_accd1b80f6/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/ECAM.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"ECAM — ECAM","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/EcoCF.html","id":null,"dir":"Reference","previous_headings":"","what":"Eco-CF — EcoCF","title":"Eco-CF — EcoCF","text":"Ecology Cystic Fibrosis (Eco-CF) study profiled microbiome pediatric CF patients. 169 pediatric cystic fibrosis patients seen four year period Columbia Univeristy Medical Center NYC, USA. 844 samples, including sputum, oral swabs bronchoalveolar lavage (BAL) fluid; V4 region 16S rRNA gene. Prospective cohort design.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/EcoCF.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Eco-CF — EcoCF","text":"","code":"EcoCF"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/EcoCF.html","id":"ecocf","dir":"Reference","previous_headings":"","what":"EcoCF","title":"Eco-CF — EcoCF","text":"MbioDataset object 77 metadata variables, 844 16S samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/EcoCF.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Eco-CF — EcoCF","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_5a4f8a1791/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/EcoCF.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Eco-CF — EcoCF","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/FARMM.html","id":null,"dir":"Reference","previous_headings":"","what":"FARMM — FARMM","title":"FARMM — FARMM","text":"Food Resulting Microbial Metabolites (FARMM) study set define impact defined diets microbiome metabolome. Follows 31 healthy human adult volunteers monitored longitudinally 15 day period. Includes 454 stool samples sequencing controls; 'shotgun' metagenomic sequencing.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/FARMM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"FARMM — FARMM","text":"","code":"FARMM"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/FARMM.html","id":"farmm","dir":"Reference","previous_headings":"","what":"FARMM","title":"FARMM — FARMM","text":"MbioDataset object 17 metadata variables, 454 shotgun stool assays 150 mass spec assays. contains following collections:  \"Metabolomics Mass spectrometry assay\" \"Shotgun metagenomics: 4th level EC metagenome abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway coverage data\"   \"Shotgun metagenomics: Genus\"  \"Shotgun metagenomics: Species\"  \"Shotgun metagenomics: Family\"  \"Shotgun metagenomics: Order\"  \"Shotgun metagenomics: Phylum\"  \"Shotgun metagenomics: Class\"   \"Shotgun metagenomics: Kingdom\"   \"Shotgun metagenomics: Normalized number taxon-specific sequence matches\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/FARMM.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"FARMM — FARMM","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_4dfda49064/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/FARMM.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"FARMM — FARMM","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/GEMS1.html","id":null,"dir":"Reference","previous_headings":"","what":"GEMS1 Case Control — GEMS1","title":"GEMS1 Case Control — GEMS1","text":"Global Enteric Multicenter Study (GEMS) investigated cause, incidence impact moderate severe diarrheal (MSD) disease children. 514 MSD cases 493 endemic controls Bangladesh, Gambia, Kenya Mali included. 1007 stool samples; V1-V2 region 16S rRNA gene. Prospective, age-stratified, matched case-control design. Additional clinical epidemiologic data participants available ClinEpiDB.org.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/GEMS1.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GEMS1 Case Control — GEMS1","text":"","code":"GEMS1"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/GEMS1.html","id":"gems-","dir":"Reference","previous_headings":"","what":"GEMS1","title":"GEMS1 Case Control — GEMS1","text":"MbioDataset object 12 metadata variables, 1015 16S stool samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/GEMS1.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"GEMS1 Case Control — GEMS1","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_a5167b81e3/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/GEMS1.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"GEMS1 Case Control — GEMS1","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_MGX.html","id":null,"dir":"Reference","previous_headings":"","what":"HMP Phase 1 Shotgun Metagenomics — HMP_MGX","title":"HMP Phase 1 Shotgun Metagenomics — HMP_MGX","text":"Human Microbiome Project (HMP) profiled microbial communities across diverse habitats human body. 103 healthly adult volunteers sampled 20 different body sites. 741 samples various types, including stool, saliva, oral, vaginal nasal swabs; 'shotgun' metagenomic sequencing.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_MGX.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"HMP Phase 1 Shotgun Metagenomics — HMP_MGX","text":"","code":"HMP_MGX"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_MGX.html","id":"hmp-mgx","dir":"Reference","previous_headings":"","what":"HMP_MGX","title":"HMP Phase 1 Shotgun Metagenomics — HMP_MGX","text":"MbioDataset object 14 metadata variables, 2145 shotgun metagenomic stool samples. contains following collections:  \"Shotgun metagenomics: 4th level EC metagenome abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway coverage data\"   \"Shotgun metagenomics: Genus\"  \"Shotgun metagenomics: Species\"  \"Shotgun metagenomics: Family\"  \"Shotgun metagenomics: Order\"  \"Shotgun metagenomics: Phylum\"  \"Shotgun metagenomics: Class\"   \"Shotgun metagenomics: Kingdom\"   \"Shotgun metagenomics: Normalized number taxon-specific sequence matches\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_MGX.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"HMP Phase 1 Shotgun Metagenomics — HMP_MGX","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_898df5869d/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_MGX.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"HMP Phase 1 Shotgun Metagenomics — HMP_MGX","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V1V3.html","id":null,"dir":"Reference","previous_headings":"","what":"HMP Phase 1 (V1-V3) — HMP_V1V3","title":"HMP Phase 1 (V1-V3) — HMP_V1V3","text":"Human Microbiome Project (HMP) profiled microbial communities across diverse habitats human body. 242 healthly adult volunteers sampled approximately 15 different body sites. 3156 samples various types; V1-V3 region 16S rRNA gene.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V1V3.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"HMP Phase 1 (V1-V3) — HMP_V1V3","text":"","code":"HMP_V1V3"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V1V3.html","id":"hmp-v-v-","dir":"Reference","previous_headings":"","what":"HMP_V1V3","title":"HMP Phase 1 (V1-V3) — HMP_V1V3","text":"MbioDataset object 11 metadata variables, 3045 16S samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V1V3.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"HMP Phase 1 (V1-V3) — HMP_V1V3","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_570856e10e/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V1V3.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"HMP Phase 1 (V1-V3) — HMP_V1V3","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V3V5.html","id":null,"dir":"Reference","previous_headings":"","what":"HMP Phase 1 (V3-V5) — HMP_V3V5","title":"HMP Phase 1 (V3-V5) — HMP_V3V5","text":"Human Microbiome Project (HMP) profiled microbial communities across diverse habitats human body. 242 healthly adult volunteers sampled approximately 15 different body sites. 5826 samples various types; V3-V5 region 16S rRNA gene.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V3V5.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"HMP Phase 1 (V3-V5) — HMP_V3V5","text":"","code":"HMP_V3V5"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V3V5.html","id":"hmp-v-v-","dir":"Reference","previous_headings":"","what":"HMP_V3V5","title":"HMP Phase 1 (V3-V5) — HMP_V3V5","text":"MbioDataset object 13 metadata variables, 5462 16S samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V3V5.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"HMP Phase 1 (V3-V5) — HMP_V3V5","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_ca4404e155/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V3V5.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"HMP Phase 1 (V3-V5) — HMP_V3V5","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Leishmaniasis.html","id":null,"dir":"Reference","previous_headings":"","what":"Human cutaneous leishmaniasis — Leishmaniasis","title":"Human cutaneous leishmaniasis — Leishmaniasis","text":"study explored skin microbiome human cutaneous leishmaniasis. 45 patients cutaneous leishmaniasis. 128 skin swabs collected affected unaffected skin; V1-V3 region 16S rRNA gene. Case-control (restrospective) design patients seen field hospital (Clinica em Leishmaniose Dr. Jackson Costa) Corte de Pedra, Bahia, Brazil.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Leishmaniasis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Human cutaneous leishmaniasis — Leishmaniasis","text":"","code":"Leishmaniasis"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Leishmaniasis.html","id":"leishmaniasis","dir":"Reference","previous_headings":"","what":"Leishmaniasis","title":"Human cutaneous leishmaniasis — Leishmaniasis","text":"MbioDataset object 16 metadata variables, 128 16S samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Leishmaniasis.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Human cutaneous leishmaniasis — Leishmaniasis","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_75221fce95/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Leishmaniasis.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Human cutaneous leishmaniasis — Leishmaniasis","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_2yr.html","id":null,"dir":"Reference","previous_headings":"","what":"MAL-ED 0-2yr — MALED_2yr","title":"MAL-ED 0-2yr — MALED_2yr","text":"study set define normal maturation gut microbiome first 2 years postnatal life. 50 children four sites MAL-ED study: Brazil, India, Peru South Africa. 1091 stool samples; V4 region 16S rRNA gene. Prospective cohort design monthly sampling first ~2 years life. Additional clinical epidemiologic data participants available ClinEpiDB.org.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_2yr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MAL-ED 0-2yr — MALED_2yr","text":"","code":"MALED_2yr"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_2yr.html","id":"maled-yr","dir":"Reference","previous_headings":"","what":"MALED_2yr","title":"MAL-ED 0-2yr — MALED_2yr","text":"MbioDataset object 16 metadata variables, 1091 16S stool samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_2yr.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"MAL-ED 0-2yr — MALED_2yr","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_72c94486c6/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_2yr.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"MAL-ED 0-2yr — MALED_2yr","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_diarrhea.html","id":null,"dir":"Reference","previous_headings":"","what":"MAL-ED diarrhea — MALED_diarrhea","title":"MAL-ED diarrhea — MALED_diarrhea","text":"study set define consequence diarrhea maturation gut microbiome first 2 years postnatal life. 271 children Amazonian lowlands near Iquitos, Peru 928 stool samples; V4 region 16S rRNA gene. Prospective cohort design samples obtained postnatal months 6, 12, 18, 24 Additional clinical epidemiologic data participants available ClinEpiDB.org.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_diarrhea.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MAL-ED diarrhea — MALED_diarrhea","text":"","code":"MALED_diarrhea"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_diarrhea.html","id":"maled-diarrhea","dir":"Reference","previous_headings":"","what":"MALED_diarrhea","title":"MAL-ED diarrhea — MALED_diarrhea","text":"MbioDataset object 36 metadata variables, 928 16S stool samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_diarrhea.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"MAL-ED diarrhea — MALED_diarrhea","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_2e56313a65/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_diarrhea.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"MAL-ED diarrhea — MALED_diarrhea","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MORDOR.html","id":null,"dir":"Reference","previous_headings":"","what":"MORDOR phase 1 — MORDOR","title":"MORDOR phase 1 — MORDOR","text":"Macrolides Oraux pour Réduire les Décès avec un Oeil sur la Résistance (MORDOR) metagenome study evaluated impact mass azithromycin administration gut microbiome children 574 pediatric (preschool) participants 30 Nigerien communities Rectal swabs; 'shotgun' metagenomic sequencing RNA.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MORDOR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MORDOR phase 1 — MORDOR","text":"","code":"MORDOR"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MORDOR.html","id":"mordor","dir":"Reference","previous_headings":"","what":"MORDOR","title":"MORDOR phase 1 — MORDOR","text":"MbioDataset object 10 metadata variables, 574 shotgun stool samples. contains following collections:  \"Shotgun metagenomics: 4th level EC metagenome abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway abundance data\"  \"Shotgun metagenomics: Metagenomeenzyme pathway coverage data\"   \"Shotgun metagenomics: Genus\"  \"Shotgun metagenomics: Species\"  \"Shotgun metagenomics: Family\"  \"Shotgun metagenomics: Order\"  \"Shotgun metagenomics: Phylum\"  \"Shotgun metagenomics: Class\"   \"Shotgun metagenomics: Kingdom\"   \"Shotgun metagenomics: Normalized number taxon-specific sequence matches\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MORDOR.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"MORDOR phase 1 — MORDOR","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_39d3629e79/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MORDOR.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"MORDOR phase 1 — MORDOR","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Malaysia_helminth.html","id":null,"dir":"Reference","previous_headings":"","what":"Malaysia helminth — Malaysia_helminth","title":"Malaysia helminth — Malaysia_helminth","text":"Malaysia Helminth study profiled gut metagenomes indigenous non-indigenous individuals originating 5 villages 407 adult pediatric participants 5 villages (Bangkong, Tanjung Sepat, Rasau, Legong, Judah), Kuala Lumpur 650 stool samples; 'shotgun' metagenomic sequencing.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Malaysia_helminth.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Malaysia helminth — Malaysia_helminth","text":"","code":"Malaysia_helminth"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Malaysia_helminth.html","id":"malaysia-helminth","dir":"Reference","previous_headings":"","what":"Malaysia_helminth","title":"Malaysia helminth — Malaysia_helminth","text":"MbioDataset object 28 metadata variables, 650 shotgun stool samples. contains following collections:  \"Shotgun metagenomics: 4th level EC metagenome abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway coverage data\"   \"Shotgun metagenomics: Genus\"  \"Shotgun metagenomics: Species\"  \"Shotgun metagenomics: Family\"  \"Shotgun metagenomics: Order\"  \"Shotgun metagenomics: Phylum\"  \"Shotgun metagenomics: Class\"   \"Shotgun metagenomics: Kingdom\"   \"Shotgun metagenomics: Normalized number taxon-specific sequence matches\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Malaysia_helminth.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Malaysia helminth — Malaysia_helminth","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_abcf1b1d90/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Malaysia_helminth.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Malaysia helminth — Malaysia_helminth","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/NICU_NEC.html","id":null,"dir":"Reference","previous_headings":"","what":"NICU-NEC — NICU_NEC","title":"NICU-NEC — NICU_NEC","text":"Neonatal Intensive Care Unit, Necrotizing Enterocolitis (NICU NEC) study set understand microbial factors associated NEC onset 150 infants born prematurely sampled perinatally high frequency first weeks months life Prospective cohort design.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/NICU_NEC.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"NICU-NEC — NICU_NEC","text":"","code":"NICU_NEC"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/NICU_NEC.html","id":"nicu-nec","dir":"Reference","previous_headings":"","what":"NICU_NEC","title":"NICU-NEC — NICU_NEC","text":"MbioDataset object 46 metadata variables, 1118 shotgun metagenomic stool samples. contains following collections:  \"Shotgun metagenomics: 4th level EC metagenome abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway coverage data\"   \"Shotgun metagenomics: Genus\"  \"Shotgun metagenomics: Species\"  \"Shotgun metagenomics: Family\"  \"Shotgun metagenomics: Order\"  \"Shotgun metagenomics: Phylum\"  \"Shotgun metagenomics: Class\"   \"Shotgun metagenomics: Kingdom\"   \"Shotgun metagenomics: Normalized number taxon-specific sequence matches\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/NICU_NEC.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"NICU-NEC — NICU_NEC","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_84fcb69f4e/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/NICU_NEC.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"NICU-NEC — NICU_NEC","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PIH_Uganda.html","id":null,"dir":"Reference","previous_headings":"","what":"PIH Uganda — PIH_Uganda","title":"PIH Uganda — PIH_Uganda","text":"study profiled microbes present cerebrospinal fluid (CSF) pediatric patients infectious non-infectious hydrocephalus. 92 children Uganda, including 58 postinfectious hydrocephalus (PIH) 34 non-postinfectious hydrocephalus (NPIH). 92 cerebrospinal fluid (CSF) samples retained workflow; V1-V2 region 16S rRNA gene. Case-control (retrospective) design samples collected first ~100 days life.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PIH_Uganda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"PIH Uganda — PIH_Uganda","text":"","code":"PIH_Uganda"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PIH_Uganda.html","id":"pih-uganda","dir":"Reference","previous_headings":"","what":"PIH_Uganda","title":"PIH Uganda — PIH_Uganda","text":"MbioDataset object 11 metadata variables, 92 CSF samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PIH_Uganda.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"PIH Uganda — PIH_Uganda","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_d00b1afb83/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PIH_Uganda.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"PIH Uganda — PIH_Uganda","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome1.html","id":null,"dir":"Reference","previous_headings":"","what":"Preterm Infant Resistome 1 — PretermInfantResistome1","title":"Preterm Infant Resistome 1 — PretermInfantResistome1","text":"Preterm Infant Resistome study used 16S rRNA marker gene sequencing shotgun metagenomics profile stool metagenome preterm infants (born < 33 weeks gestational age) stratified antibiotic use hospitalization. 84 preterm infant patients seen Washington University School Medicine St. Louis, MO, USA. 399 stool samples; 'shotgun' metagenomic sequencing. 103/399 stool samples; V4 16S rRNA gene sequencing. Prospective cohort design.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome1.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Preterm Infant Resistome 1 — PretermInfantResistome1","text":"","code":"PretermInfantResistome1"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome1.html","id":"preterminfantresistome-","dir":"Reference","previous_headings":"","what":"PretermInfantResistome1","title":"Preterm Infant Resistome 1 — PretermInfantResistome1","text":"MbioDataset object 64 metadata variables, 399 shotgun stool samples, 103 16S stool samples. contains following collections:  \"Shotgun metagenomics: 4th level EC metagenome abundance data\"  \"Shotgun metagenomics: Metagenomeenzyme pathway abundance data\"  \"Shotgun metagenomics: Metagenomeenzyme pathway coverage data\"   \"Shotgun metagenomics: Genus\"  \"Shotgun metagenomics: Species\"  \"Shotgun metagenomics: Family\"  \"Shotgun metagenomics: Order\"  \"Shotgun metagenomics: Phylum\"  \"Shotgun metagenomics: Class\"   \"Shotgun metagenomics: Kingdom\"   \"Shotgun metagenomics: Normalized number taxon-specific sequence matches\"  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome1.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Preterm Infant Resistome 1 — PretermInfantResistome1","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_d1b9f788dc/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome1.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Preterm Infant Resistome 1 — PretermInfantResistome1","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome2.html","id":null,"dir":"Reference","previous_headings":"","what":"Preterm Infant Resistome 1 — PretermInfantResistome2","title":"Preterm Infant Resistome 1 — PretermInfantResistome2","text":"Preterm Infant Resistome II study profiled stool metagenome preterm infants (born < 33 weeks gestational age) throughout first 21 months life. Patients stratified antibiotic use hospitalization 41 preterm infants 17 antibiotic-naive, healthy early term late-preterm infants seen Washington University School Medicine St. Louis, MO, USA 437 stool samples; 'shotgun' metagenomic sequencing. Prospective cohort design.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Preterm Infant Resistome 1 — PretermInfantResistome2","text":"","code":"PretermInfantResistome2"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome2.html","id":"preterminfantresistome-","dir":"Reference","previous_headings":"","what":"PretermInfantResistome2","title":"Preterm Infant Resistome 1 — PretermInfantResistome2","text":"MbioDataset object 24 metadata variables, 427 shotgun stool samples. contains following collections:  \"Shotgun metagenomics: 4th level EC metagenome abundance data\"  \"Shotgun metagenomics: Metagenomeenzyme pathway abundance data\"  \"Shotgun metagenomics: Metagenomeenzyme pathway coverage data\"   \"Shotgun metagenomics: Genus\"  \"Shotgun metagenomics: Species\"  \"Shotgun metagenomics: Family\"  \"Shotgun metagenomics: Order\"  \"Shotgun metagenomics: Phylum\"  \"Shotgun metagenomics: Class\"   \"Shotgun metagenomics: Kingdom\"   \"Shotgun metagenomics: Normalized number taxon-specific sequence matches\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome2.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Preterm Infant Resistome 1 — PretermInfantResistome2","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_b9dc726b20/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome2.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Preterm Infant Resistome 1 — PretermInfantResistome2","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/UgandaMaternal.html","id":null,"dir":"Reference","previous_headings":"","what":"Uganda Maternal — UgandaMaternal","title":"Uganda Maternal — UgandaMaternal","text":"Uganda Maternal microbiome study profled vaginal samples obtained Ugandan pregnant women active labor birth. Patients catergorizd intrapartum fever status 99 adult intrapartum women seen Mbarara (n=50) Mbale (n=49) Hospitals western eastern Uganda, respectively 99 vaginal swab samples; profiled using V1-V2 V3-V4 region 16S rRNA gene.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/UgandaMaternal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Uganda Maternal — UgandaMaternal","text":"","code":"UgandaMaternal"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/UgandaMaternal.html","id":"ugandamaternal","dir":"Reference","previous_headings":"","what":"UgandaMaternal","title":"Uganda Maternal — UgandaMaternal","text":"MbioDataset object 11 metadata variables, 99 successful V1V2 assays 97 successful V3V4 assays. contains following collections:  \"16S V1V2 Order\"  \"16S V1V2 Genus\"  \"16S V1V2 Family\"  \"16S V1V2 Species\"  \"16S V1V2 Class\"  \"16S V1V2 Phylum\"  \"16S V1V2 Kingdom\"  \"16S V3V4 Order\"  \"16S V3V4 Genus\"  \"16S V3V4 Family\"  \"16S V3V4 Species\"  \"16S V3V4 Class\"  \"16S V3V4 Phylum\"  \"16S V3V4 Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/UgandaMaternal.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Uganda Maternal — UgandaMaternal","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_d3053dfc9c/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/UgandaMaternal.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Uganda Maternal — UgandaMaternal","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/getCuratedDatasetNames.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Curated Data Set Names — getCuratedDatasetNames","title":"Get Curated Data Set Names — getCuratedDatasetNames","text":"Returns vector curated data set names 'microbiomeData' package. data MicrobiomeDB.org website can analyzed 'MicrobiomeDB' R package.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/getCuratedDatasetNames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Curated Data Set Names — getCuratedDatasetNames","text":"","code":"getCuratedDatasetNames()"},{"path":"https://microbiomedb.github.io/microbiomeData/reference/getCuratedDatasetNames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Curated Data Set Names — getCuratedDatasetNames","text":"vector curated data set names","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/microbiomeData-package.html","id":null,"dir":"Reference","previous_headings":"","what":"microbiomeData: Curated Data from MicrobiomeDB.org — microbiomeData-package","title":"microbiomeData: Curated Data from MicrobiomeDB.org — microbiomeData-package","text":"R package containing curated datasets MicrobiomeDB.org.","code":""},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/microbiomeData-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"microbiomeData: Curated Data from MicrobiomeDB.org — microbiomeData-package","text":"Maintainer: Danielle Callan dcallan@upenn.edu","code":""}]
+[{"path":"https://microbiomedb.github.io/microbiomeData/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"Apache License","title":"Apache License","text":"Version 2.0, January 2004 <http://www.apache.org/licenses/>","code":""},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/LICENSE.html","id":"id_1-definitions","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"1. Definitions","title":"Apache License","text":"“License” shall mean terms conditions use, reproduction, distribution defined Sections 1 9 document. “Licensor” shall mean copyright owner entity authorized copyright owner granting License. “Legal Entity” shall mean union acting entity entities control, controlled , common control entity. purposes definition, “control” means () power, direct indirect, cause direction management entity, whether contract otherwise, (ii) ownership fifty percent (50%) outstanding shares, (iii) beneficial ownership entity. “” (“”) shall mean individual Legal Entity exercising permissions granted License. “Source” form shall mean preferred form making modifications, including limited software source code, documentation source, configuration files. “Object” form shall mean form resulting mechanical transformation translation Source form, including limited compiled object code, generated documentation, conversions media types. “Work” shall mean work authorship, whether Source Object form, made available License, indicated copyright notice included attached work (example provided Appendix ). “Derivative Works” shall mean work, whether Source Object form, based (derived ) Work editorial revisions, annotations, elaborations, modifications represent, whole, original work authorship. purposes License, Derivative Works shall include works remain separable , merely link (bind name) interfaces , Work Derivative Works thereof. “Contribution” shall mean work authorship, including original version Work modifications additions Work Derivative Works thereof, intentionally submitted Licensor inclusion Work copyright owner individual Legal Entity authorized submit behalf copyright owner. purposes definition, “submitted” means form electronic, verbal, written communication sent Licensor representatives, including limited communication electronic mailing lists, source code control systems, issue tracking systems managed , behalf , Licensor purpose discussing improving Work, excluding communication conspicuously marked otherwise designated writing copyright owner “Contribution.” “Contributor” shall mean Licensor individual Legal Entity behalf Contribution received Licensor subsequently incorporated within Work.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/LICENSE.html","id":"id_2-grant-of-copyright-license","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"2. 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Redistribution","title":"Apache License","text":"may reproduce distribute copies Work Derivative Works thereof medium, without modifications, Source Object form, provided meet following conditions: () must give recipients Work Derivative Works copy License; (b) must cause modified files carry prominent notices stating changed files; (c) must retain, Source form Derivative Works distribute, copyright, patent, trademark, attribution notices Source form Work, excluding notices pertain part Derivative Works; (d) Work includes “NOTICE” text file part distribution, Derivative Works distribute must include readable copy attribution notices contained within NOTICE file, excluding notices pertain part Derivative Works, least one following places: within NOTICE text file distributed part Derivative Works; within Source form documentation, provided along Derivative Works; , within display generated Derivative Works, wherever third-party notices normally appear. contents NOTICE file informational purposes modify License. may add attribution notices within Derivative Works distribute, alongside addendum NOTICE text Work, provided additional attribution notices construed modifying License. may add copyright statement modifications may provide additional different license terms conditions use, reproduction, distribution modifications, Derivative Works whole, provided use, reproduction, distribution Work otherwise complies conditions stated License.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/LICENSE.html","id":"id_5-submission-of-contributions","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"5. Submission of Contributions","title":"Apache License","text":"Unless explicitly state otherwise, Contribution intentionally submitted inclusion Work Licensor shall terms conditions License, without additional terms conditions. Notwithstanding , nothing herein shall supersede modify terms separate license agreement may executed Licensor regarding Contributions.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/LICENSE.html","id":"id_6-trademarks","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"6. 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Disclaimer of Warranty","title":"Apache License","text":"Unless required applicable law agreed writing, Licensor provides Work (Contributor provides Contributions) “” BASIS, WITHOUT WARRANTIES CONDITIONS KIND, either express implied, including, without limitation, warranties conditions TITLE, NON-INFRINGEMENT, MERCHANTABILITY, FITNESS PARTICULAR PURPOSE. solely responsible determining appropriateness using redistributing Work assume risks associated exercise permissions License.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/LICENSE.html","id":"id_8-limitation-of-liability","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"8. Limitation of Liability","title":"Apache License","text":"event legal theory, whether tort (including negligence), contract, otherwise, unless required applicable law (deliberate grossly negligent acts) agreed writing, shall Contributor liable damages, including direct, indirect, special, incidental, consequential damages character arising result License use inability use Work (including limited damages loss goodwill, work stoppage, computer failure malfunction, commercial damages losses), even Contributor advised possibility damages.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/LICENSE.html","id":"id_9-accepting-warranty-or-additional-liability","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"9. Accepting Warranty or Additional Liability","title":"Apache License","text":"redistributing Work Derivative Works thereof, may choose offer, charge fee , acceptance support, warranty, indemnity, liability obligations /rights consistent License. However, accepting obligations, may act behalf sole responsibility, behalf Contributor, agree indemnify, defend, hold Contributor harmless liability incurred , claims asserted , Contributor reason accepting warranty additional liability. END TERMS CONDITIONS","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/LICENSE.html","id":"appendix-how-to-apply-the-apache-license-to-your-work","dir":"","previous_headings":"","what":"APPENDIX: How to apply the Apache License to your work","title":"Apache License","text":"apply Apache License work, attach following boilerplate notice, fields enclosed brackets [] replaced identifying information. (Don’t include brackets!) text enclosed appropriate comment syntax file format. also recommend file class name description purpose included “printed page” copyright notice easier identification within third-party archives.","code":"Copyright [yyyy] [name of copyright owner]  Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at    http://www.apache.org/licenses/LICENSE-2.0  Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License."},{"path":"https://microbiomedb.github.io/microbiomeData/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Danielle Callan. Author, maintainer.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Callan D (2024). microbiomeData: Curated Data MicrobiomeDB.org. R package version 1.0.4, https://microbiomedb.github.io/microbiomeData/, https://github.com/microbiomeDB/microbiomeData.","code":"@Manual{,   title = {microbiomeData: Curated Data from MicrobiomeDB.org},   author = {Danielle Callan},   year = {2024},   note = {R package version 1.0.4, https://microbiomedb.github.io/microbiomeData/},   url = {https://github.com/microbiomeDB/microbiomeData}, }"},{"path":"https://microbiomedb.github.io/microbiomeData/index.html","id":"microbiomedata","dir":"","previous_headings":"","what":"Curated Data from MicrobiomeDB.org","title":"Curated Data from MicrobiomeDB.org","text":"R package containing curated datasets MicrobiomeDB.org helper function list datasets available.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Curated Data from MicrobiomeDB.org","text":"Use R package remotes install microbiomeData. R command prompt:","code":"remotes::install_github('microbiomeDB/microbiomeData')"},{"path":"https://microbiomedb.github.io/microbiomeData/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Curated Data from MicrobiomeDB.org","text":"package contains curated datasets MicrobiomeDB.org. extension MicrobiomeDB R package can used analyze visualize data. package installed attached one.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/index.html","id":"direct-usage","dir":"","previous_headings":"Usage","what":"Direct Usage","title":"Curated Data from MicrobiomeDB.org","text":"can get list curated datasets available within package following: favorite dataset myData, can ask specific collections dataset. collection group variables represent biologically coherent concept measured comparable range. Relative abundances specific taxonomic rank example. might look something like:","code":"microbiomeData::getCuratedDatsetNames() myData <- microbiomeData::DiabImmune getCollectionNames(myData) # will print the names of collections myCollection <- getCollection(myData, '16S (V4) Species')"},{"path":"https://microbiomedb.github.io/microbiomeData/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Curated Data from MicrobiomeDB.org","text":"Apache 2.0","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Anopheles_albimanus.html","id":null,"dir":"Reference","previous_headings":"","what":"Anopheles albimanus — Anopheles_albimanus","title":"Anopheles albimanus — Anopheles_albimanus","text":"study assessed impact pyrethroid exposure internal cuticle microbiome Anopheles albimanusi. 125 samples, pool 3 mosquitos. V3-V4 region 16S rRNA gene. Adult larval Anopheles albimanus collected around Las Cruces, Guatemala.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Anopheles_albimanus.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Anopheles albimanus — Anopheles_albimanus","text":"","code":"Anopheles_albimanus"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Anopheles_albimanus.html","id":"anopheles-albimanus","dir":"Reference","previous_headings":"","what":"Anopheles_albimanus","title":"Anopheles albimanus — Anopheles_albimanus","text":"MbioDataset object 12 metadata variables, 125 16S samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Anopheles_albimanus.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Anopheles albimanus — Anopheles_albimanus","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_36cb9bab56/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Anopheles_albimanus.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Anopheles albimanus — Anopheles_albimanus","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/BONUS.html","id":null,"dir":"Reference","previous_headings":"","what":"BONUS-CF — BONUS","title":"BONUS-CF — BONUS","text":"Baby Observational Nutrition Study (BONUS) set identify microbial correlates poor growth observed infants cystic fibrosis (CF) 207 infants diagnosed cystic fibrosis newborn screening Shotgun metagenomic sequencing 122 samples collected healthy controls, 1157 stool samples infants CF collected months 3, 4, 5, 6, 8, 10 12 life Longitudinal, observational, multicenter cohort study.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/BONUS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"BONUS-CF — BONUS","text":"","code":"BONUS"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/BONUS.html","id":"bonus","dir":"Reference","previous_headings":"","what":"BONUS","title":"BONUS-CF — BONUS","text":"MbioDataset object 23 metadata variables, 1279 shotgun metagenomic stool samples. contains following collections:  \"Shotgun metagenomics: 4th level EC metagenome abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway coverage data\"   \"Shotgun metagenomics: Genus\"  \"Shotgun metagenomics: Species\"  \"Shotgun metagenomics: Family\"  \"Shotgun metagenomics: Order\"  \"Shotgun metagenomics: Phylum\"  \"Shotgun metagenomics: Class\"   \"Shotgun metagenomics: Kingdom\"   \"Shotgun metagenomics: Normalized number taxon-specific sequence matches\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/BONUS.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"BONUS-CF — BONUS","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_b3b3ae9838/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/BONUS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"BONUS-CF — BONUS","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Bangladesh.html","id":null,"dir":"Reference","previous_headings":"","what":"Bangladesh 5yr — Bangladesh","title":"Bangladesh 5yr — Bangladesh","text":"study set define normal maturation gut microbiome first 5 years postnatal life. 55 members birth cohort consistently healthy anthropometric scores living within Mirpur district Dhaka, Bangladesh. 2415 stool samples; V4 region 16S rRNA gene. Prospective cohort design monthly sampling first ~5 years life.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Bangladesh.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bangladesh 5yr — Bangladesh","text":"","code":"Bangladesh"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Bangladesh.html","id":"bangladesh","dir":"Reference","previous_headings":"","what":"Bangladesh","title":"Bangladesh 5yr — Bangladesh","text":"MbioDataset object 14 metadata variables, 2145 16S stool samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Bangladesh.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Bangladesh 5yr — Bangladesh","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_1102462e80/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Bangladesh.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Bangladesh 5yr — Bangladesh","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/DailyBaby.html","id":null,"dir":"Reference","previous_headings":"","what":"DailyBaby — DailyBaby","title":"DailyBaby — DailyBaby","text":"Near daily fecal specimens collected term infants first year life. 12 healthy term infants born Oslo, Norway. 2684 stool samples total, average 224 samples (range 116–267) per infant. Prospective cohort design.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/DailyBaby.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DailyBaby — DailyBaby","text":"","code":"DailyBaby"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/DailyBaby.html","id":"dailybaby","dir":"Reference","previous_headings":"","what":"DailyBaby","title":"DailyBaby — DailyBaby","text":"MbioDataset object 17 metadata variables, 2684 16S stool samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/DailyBaby.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"DailyBaby — DailyBaby","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_5a4f8a1791/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/DailyBaby.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"DailyBaby — DailyBaby","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/DiabImmune.html","id":null,"dir":"Reference","previous_headings":"","what":"DiabImmune — DiabImmune","title":"DiabImmune — DiabImmune","text":"Broad Institute's study three pediatric cohorts examined microbiome children high risk development Type 1 diabetes (T1D). Includes 289 children across three sites, including Russia (Karelia), Finland Estonia. 3184 stool samples amplicon sequencing data V4 region 16S rRNA gene. 1149 stool samples 'shotgun' metagenomic sequencing data. Prospective cohort design monthly sampling first ~3 years life. Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/DiabImmune.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DiabImmune — DiabImmune","text":"","code":"DiabImmune"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/DiabImmune.html","id":"diabimmune","dir":"Reference","previous_headings":"","what":"DiabImmune","title":"DiabImmune — DiabImmune","text":"MbioDataset object 60 metadata variables, 3184 16S stool samples 1149 shotgun stool samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"  \"Shotgun metagenomics: 4th level EC metagenome abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway coverage data\"   \"Shotgun metagenomics: Genus\"  \"Shotgun metagenomics: Species\"  \"Shotgun metagenomics: Family\"  \"Shotgun metagenomics: Order\"  \"Shotgun metagenomics: Phylum\"  \"Shotgun metagenomics: Class\"   \"Shotgun metagenomics: Kingdom\"   \"Shotgun metagenomics: Normalized number taxon-specific sequence matches\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/DiabImmune.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"DiabImmune — DiabImmune","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_a2f8877e68/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/ECAM.html","id":null,"dir":"Reference","previous_headings":"","what":"ECAM — ECAM","title":"ECAM — ECAM","text":"Early Childhood Antibiotics Microbiome (ECAM) study set identify impact antibiotics, delivery mode diet infant gut Microbiome. Prospective cohort design healthy humans USA. 43 infants sampled first two years life. 1216 samples various types; V4 region 16S rRNA gene.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/ECAM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ECAM — ECAM","text":"","code":"ECAM"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/ECAM.html","id":"ecam","dir":"Reference","previous_headings":"","what":"ECAM","title":"ECAM — ECAM","text":"MbioDataset object 27 metadata variables, 1216 16S samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/ECAM.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"ECAM — ECAM","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_accd1b80f6/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/ECAM.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"ECAM — ECAM","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/EcoCF.html","id":null,"dir":"Reference","previous_headings":"","what":"Eco-CF — EcoCF","title":"Eco-CF — EcoCF","text":"Ecology Cystic Fibrosis (Eco-CF) study profiled microbiome pediatric CF patients. 169 pediatric cystic fibrosis patients seen four year period Columbia Univeristy Medical Center NYC, USA. 844 samples, including sputum, oral swabs bronchoalveolar lavage (BAL) fluid; V4 region 16S rRNA gene. Prospective cohort design.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/EcoCF.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Eco-CF — EcoCF","text":"","code":"EcoCF"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/EcoCF.html","id":"ecocf","dir":"Reference","previous_headings":"","what":"EcoCF","title":"Eco-CF — EcoCF","text":"MbioDataset object 77 metadata variables, 844 16S samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/EcoCF.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Eco-CF — EcoCF","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_5a4f8a1791/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/EcoCF.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Eco-CF — EcoCF","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/FARMM.html","id":null,"dir":"Reference","previous_headings":"","what":"FARMM — FARMM","title":"FARMM — FARMM","text":"Food Resulting Microbial Metabolites (FARMM) study set define impact defined diets microbiome metabolome. Follows 31 healthy human adult volunteers monitored longitudinally 15 day period. Includes 454 stool samples sequencing controls; 'shotgun' metagenomic sequencing.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/FARMM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"FARMM — FARMM","text":"","code":"FARMM"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/FARMM.html","id":"farmm","dir":"Reference","previous_headings":"","what":"FARMM","title":"FARMM — FARMM","text":"MbioDataset object 17 metadata variables, 454 shotgun stool assays 150 mass spec assays. contains following collections:  \"Metabolomics Mass spectrometry assay\" \"Shotgun metagenomics: 4th level EC metagenome abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway coverage data\"   \"Shotgun metagenomics: Genus\"  \"Shotgun metagenomics: Species\"  \"Shotgun metagenomics: Family\"  \"Shotgun metagenomics: Order\"  \"Shotgun metagenomics: Phylum\"  \"Shotgun metagenomics: Class\"   \"Shotgun metagenomics: Kingdom\"   \"Shotgun metagenomics: Normalized number taxon-specific sequence matches\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/FARMM.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"FARMM — FARMM","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_4dfda49064/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/FARMM.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"FARMM — FARMM","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/GEMS1.html","id":null,"dir":"Reference","previous_headings":"","what":"GEMS1 Case Control — GEMS1","title":"GEMS1 Case Control — GEMS1","text":"Global Enteric Multicenter Study (GEMS) investigated cause, incidence impact moderate severe diarrheal (MSD) disease children. 514 MSD cases 493 endemic controls Bangladesh, Gambia, Kenya Mali included. 1007 stool samples; V1-V2 region 16S rRNA gene. Prospective, age-stratified, matched case-control design. Additional clinical epidemiologic data participants available ClinEpiDB.org.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/GEMS1.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GEMS1 Case Control — GEMS1","text":"","code":"GEMS1"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/GEMS1.html","id":"gems-","dir":"Reference","previous_headings":"","what":"GEMS1","title":"GEMS1 Case Control — GEMS1","text":"MbioDataset object 12 metadata variables, 1015 16S stool samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/GEMS1.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"GEMS1 Case Control — GEMS1","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_a5167b81e3/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/GEMS1.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"GEMS1 Case Control — GEMS1","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_MGX.html","id":null,"dir":"Reference","previous_headings":"","what":"HMP Phase 1 Shotgun Metagenomics — HMP_MGX","title":"HMP Phase 1 Shotgun Metagenomics — HMP_MGX","text":"Human Microbiome Project (HMP) profiled microbial communities across diverse habitats human body. 103 healthly adult volunteers sampled 20 different body sites. 741 samples various types, including stool, saliva, oral, vaginal nasal swabs; 'shotgun' metagenomic sequencing.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_MGX.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"HMP Phase 1 Shotgun Metagenomics — HMP_MGX","text":"","code":"HMP_MGX"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_MGX.html","id":"hmp-mgx","dir":"Reference","previous_headings":"","what":"HMP_MGX","title":"HMP Phase 1 Shotgun Metagenomics — HMP_MGX","text":"MbioDataset object 14 metadata variables, 2145 shotgun metagenomic stool samples. contains following collections:  \"Shotgun metagenomics: 4th level EC metagenome abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway coverage data\"   \"Shotgun metagenomics: Genus\"  \"Shotgun metagenomics: Species\"  \"Shotgun metagenomics: Family\"  \"Shotgun metagenomics: Order\"  \"Shotgun metagenomics: Phylum\"  \"Shotgun metagenomics: Class\"   \"Shotgun metagenomics: Kingdom\"   \"Shotgun metagenomics: Normalized number taxon-specific sequence matches\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_MGX.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"HMP Phase 1 Shotgun Metagenomics — HMP_MGX","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_898df5869d/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_MGX.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"HMP Phase 1 Shotgun Metagenomics — HMP_MGX","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V1V3.html","id":null,"dir":"Reference","previous_headings":"","what":"HMP Phase 1 (V1-V3) — HMP_V1V3","title":"HMP Phase 1 (V1-V3) — HMP_V1V3","text":"Human Microbiome Project (HMP) profiled microbial communities across diverse habitats human body. 242 healthly adult volunteers sampled approximately 15 different body sites. 3156 samples various types; V1-V3 region 16S rRNA gene.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V1V3.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"HMP Phase 1 (V1-V3) — HMP_V1V3","text":"","code":"HMP_V1V3"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V1V3.html","id":"hmp-v-v-","dir":"Reference","previous_headings":"","what":"HMP_V1V3","title":"HMP Phase 1 (V1-V3) — HMP_V1V3","text":"MbioDataset object 11 metadata variables, 3045 16S samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V1V3.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"HMP Phase 1 (V1-V3) — HMP_V1V3","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_570856e10e/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V1V3.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"HMP Phase 1 (V1-V3) — HMP_V1V3","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V3V5.html","id":null,"dir":"Reference","previous_headings":"","what":"HMP Phase 1 (V3-V5) — HMP_V3V5","title":"HMP Phase 1 (V3-V5) — HMP_V3V5","text":"Human Microbiome Project (HMP) profiled microbial communities across diverse habitats human body. 242 healthly adult volunteers sampled approximately 15 different body sites. 5826 samples various types; V3-V5 region 16S rRNA gene.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V3V5.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"HMP Phase 1 (V3-V5) — HMP_V3V5","text":"","code":"HMP_V3V5"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V3V5.html","id":"hmp-v-v-","dir":"Reference","previous_headings":"","what":"HMP_V3V5","title":"HMP Phase 1 (V3-V5) — HMP_V3V5","text":"MbioDataset object 13 metadata variables, 5462 16S samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V3V5.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"HMP Phase 1 (V3-V5) — HMP_V3V5","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_ca4404e155/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/HMP_V3V5.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"HMP Phase 1 (V3-V5) — HMP_V3V5","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Leishmaniasis.html","id":null,"dir":"Reference","previous_headings":"","what":"Human cutaneous leishmaniasis — Leishmaniasis","title":"Human cutaneous leishmaniasis — Leishmaniasis","text":"study explored skin microbiome human cutaneous leishmaniasis. 45 patients cutaneous leishmaniasis. 128 skin swabs collected affected unaffected skin; V1-V3 region 16S rRNA gene. Case-control (restrospective) design patients seen field hospital (Clinica em Leishmaniose Dr. Jackson Costa) Corte de Pedra, Bahia, Brazil.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Leishmaniasis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Human cutaneous leishmaniasis — Leishmaniasis","text":"","code":"Leishmaniasis"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Leishmaniasis.html","id":"leishmaniasis","dir":"Reference","previous_headings":"","what":"Leishmaniasis","title":"Human cutaneous leishmaniasis — Leishmaniasis","text":"MbioDataset object 16 metadata variables, 128 16S samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Leishmaniasis.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Human cutaneous leishmaniasis — Leishmaniasis","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_75221fce95/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Leishmaniasis.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Human cutaneous leishmaniasis — Leishmaniasis","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_2yr.html","id":null,"dir":"Reference","previous_headings":"","what":"MAL-ED 0-2yr — MALED_2yr","title":"MAL-ED 0-2yr — MALED_2yr","text":"study set define normal maturation gut microbiome first 2 years postnatal life. 50 children four sites MAL-ED study: Brazil, India, Peru South Africa. 1091 stool samples; V4 region 16S rRNA gene. Prospective cohort design monthly sampling first ~2 years life. Additional clinical epidemiologic data participants available ClinEpiDB.org.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_2yr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MAL-ED 0-2yr — MALED_2yr","text":"","code":"MALED_2yr"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_2yr.html","id":"maled-yr","dir":"Reference","previous_headings":"","what":"MALED_2yr","title":"MAL-ED 0-2yr — MALED_2yr","text":"MbioDataset object 16 metadata variables, 1091 16S stool samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_2yr.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"MAL-ED 0-2yr — MALED_2yr","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_72c94486c6/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_2yr.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"MAL-ED 0-2yr — MALED_2yr","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_diarrhea.html","id":null,"dir":"Reference","previous_headings":"","what":"MAL-ED diarrhea — MALED_diarrhea","title":"MAL-ED diarrhea — MALED_diarrhea","text":"study set define consequence diarrhea maturation gut microbiome first 2 years postnatal life. 271 children Amazonian lowlands near Iquitos, Peru 928 stool samples; V4 region 16S rRNA gene. Prospective cohort design samples obtained postnatal months 6, 12, 18, 24 Additional clinical epidemiologic data participants available ClinEpiDB.org.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_diarrhea.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MAL-ED diarrhea — MALED_diarrhea","text":"","code":"MALED_diarrhea"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_diarrhea.html","id":"maled-diarrhea","dir":"Reference","previous_headings":"","what":"MALED_diarrhea","title":"MAL-ED diarrhea — MALED_diarrhea","text":"MbioDataset object 36 metadata variables, 928 16S stool samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_diarrhea.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"MAL-ED diarrhea — MALED_diarrhea","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_2e56313a65/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MALED_diarrhea.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"MAL-ED diarrhea — MALED_diarrhea","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MORDOR.html","id":null,"dir":"Reference","previous_headings":"","what":"MORDOR phase 1 — MORDOR","title":"MORDOR phase 1 — MORDOR","text":"Macrolides Oraux pour Réduire les Décès avec un Oeil sur la Résistance (MORDOR) metagenome study evaluated impact mass azithromycin administration gut microbiome children 574 pediatric (preschool) participants 30 Nigerien communities Rectal swabs; 'shotgun' metagenomic sequencing RNA.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MORDOR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MORDOR phase 1 — MORDOR","text":"","code":"MORDOR"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MORDOR.html","id":"mordor","dir":"Reference","previous_headings":"","what":"MORDOR","title":"MORDOR phase 1 — MORDOR","text":"MbioDataset object 10 metadata variables, 574 shotgun stool samples. contains following collections:  \"Shotgun metagenomics: 4th level EC metagenome abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway abundance data\"  \"Shotgun metagenomics: Metagenomeenzyme pathway coverage data\"   \"Shotgun metagenomics: Genus\"  \"Shotgun metagenomics: Species\"  \"Shotgun metagenomics: Family\"  \"Shotgun metagenomics: Order\"  \"Shotgun metagenomics: Phylum\"  \"Shotgun metagenomics: Class\"   \"Shotgun metagenomics: Kingdom\"   \"Shotgun metagenomics: Normalized number taxon-specific sequence matches\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MORDOR.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"MORDOR phase 1 — MORDOR","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_39d3629e79/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/MORDOR.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"MORDOR phase 1 — MORDOR","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Malaysia_helminth.html","id":null,"dir":"Reference","previous_headings":"","what":"Malaysia helminth — Malaysia_helminth","title":"Malaysia helminth — Malaysia_helminth","text":"Malaysia Helminth study profiled gut metagenomes indigenous non-indigenous individuals originating 5 villages 407 adult pediatric participants 5 villages (Bangkong, Tanjung Sepat, Rasau, Legong, Judah), Kuala Lumpur 650 stool samples; 'shotgun' metagenomic sequencing.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Malaysia_helminth.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Malaysia helminth — Malaysia_helminth","text":"","code":"Malaysia_helminth"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Malaysia_helminth.html","id":"malaysia-helminth","dir":"Reference","previous_headings":"","what":"Malaysia_helminth","title":"Malaysia helminth — Malaysia_helminth","text":"MbioDataset object 28 metadata variables, 650 shotgun stool samples. contains following collections:  \"Shotgun metagenomics: 4th level EC metagenome abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway coverage data\"   \"Shotgun metagenomics: Genus\"  \"Shotgun metagenomics: Species\"  \"Shotgun metagenomics: Family\"  \"Shotgun metagenomics: Order\"  \"Shotgun metagenomics: Phylum\"  \"Shotgun metagenomics: Class\"   \"Shotgun metagenomics: Kingdom\"   \"Shotgun metagenomics: Normalized number taxon-specific sequence matches\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Malaysia_helminth.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Malaysia helminth — Malaysia_helminth","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_abcf1b1d90/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/Malaysia_helminth.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Malaysia helminth — Malaysia_helminth","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/NICU_NEC.html","id":null,"dir":"Reference","previous_headings":"","what":"NICU-NEC — NICU_NEC","title":"NICU-NEC — NICU_NEC","text":"Neonatal Intensive Care Unit, Necrotizing Enterocolitis (NICU NEC) study set understand microbial factors associated NEC onset 150 infants born prematurely sampled perinatally high frequency first weeks months life Prospective cohort design.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/NICU_NEC.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"NICU-NEC — NICU_NEC","text":"","code":"NICU_NEC"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/NICU_NEC.html","id":"nicu-nec","dir":"Reference","previous_headings":"","what":"NICU_NEC","title":"NICU-NEC — NICU_NEC","text":"MbioDataset object 46 metadata variables, 1118 shotgun metagenomic stool samples. contains following collections:  \"Shotgun metagenomics: 4th level EC metagenome abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway abundance data\"  \"Shotgun metagenomics: Metagenome enzyme pathway coverage data\"   \"Shotgun metagenomics: Genus\"  \"Shotgun metagenomics: Species\"  \"Shotgun metagenomics: Family\"  \"Shotgun metagenomics: Order\"  \"Shotgun metagenomics: Phylum\"  \"Shotgun metagenomics: Class\"   \"Shotgun metagenomics: Kingdom\"   \"Shotgun metagenomics: Normalized number taxon-specific sequence matches\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/NICU_NEC.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"NICU-NEC — NICU_NEC","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_84fcb69f4e/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/NICU_NEC.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"NICU-NEC — NICU_NEC","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PIH_Uganda.html","id":null,"dir":"Reference","previous_headings":"","what":"PIH Uganda — PIH_Uganda","title":"PIH Uganda — PIH_Uganda","text":"study profiled microbes present cerebrospinal fluid (CSF) pediatric patients infectious non-infectious hydrocephalus. 92 children Uganda, including 58 postinfectious hydrocephalus (PIH) 34 non-postinfectious hydrocephalus (NPIH). 92 cerebrospinal fluid (CSF) samples retained workflow; V1-V2 region 16S rRNA gene. Case-control (retrospective) design samples collected first ~100 days life.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PIH_Uganda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"PIH Uganda — PIH_Uganda","text":"","code":"PIH_Uganda"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PIH_Uganda.html","id":"pih-uganda","dir":"Reference","previous_headings":"","what":"PIH_Uganda","title":"PIH Uganda — PIH_Uganda","text":"MbioDataset object 11 metadata variables, 92 CSF samples. contains following collections:  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PIH_Uganda.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"PIH Uganda — PIH_Uganda","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_d00b1afb83/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PIH_Uganda.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"PIH Uganda — PIH_Uganda","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome1.html","id":null,"dir":"Reference","previous_headings":"","what":"Preterm Infant Resistome 1 — PretermInfantResistome1","title":"Preterm Infant Resistome 1 — PretermInfantResistome1","text":"Preterm Infant Resistome study used 16S rRNA marker gene sequencing shotgun metagenomics profile stool metagenome preterm infants (born < 33 weeks gestational age) stratified antibiotic use hospitalization. 84 preterm infant patients seen Washington University School Medicine St. Louis, MO, USA. 399 stool samples; 'shotgun' metagenomic sequencing. 103/399 stool samples; V4 16S rRNA gene sequencing. Prospective cohort design.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome1.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Preterm Infant Resistome 1 — PretermInfantResistome1","text":"","code":"PretermInfantResistome1"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome1.html","id":"preterminfantresistome-","dir":"Reference","previous_headings":"","what":"PretermInfantResistome1","title":"Preterm Infant Resistome 1 — PretermInfantResistome1","text":"MbioDataset object 64 metadata variables, 399 shotgun stool samples, 103 16S stool samples. contains following collections:  \"Shotgun metagenomics: 4th level EC metagenome abundance data\"  \"Shotgun metagenomics: Metagenomeenzyme pathway abundance data\"  \"Shotgun metagenomics: Metagenomeenzyme pathway coverage data\"   \"Shotgun metagenomics: Genus\"  \"Shotgun metagenomics: Species\"  \"Shotgun metagenomics: Family\"  \"Shotgun metagenomics: Order\"  \"Shotgun metagenomics: Phylum\"  \"Shotgun metagenomics: Class\"   \"Shotgun metagenomics: Kingdom\"   \"Shotgun metagenomics: Normalized number taxon-specific sequence matches\"  \"16S Order\"  \"16S Genus\"  \"16S Family\"  \"16S Species\"  \"16S Class\"  \"16S Phylum\"  \"16S Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome1.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Preterm Infant Resistome 1 — PretermInfantResistome1","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_d1b9f788dc/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome1.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Preterm Infant Resistome 1 — PretermInfantResistome1","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome2.html","id":null,"dir":"Reference","previous_headings":"","what":"Preterm Infant Resistome 1 — PretermInfantResistome2","title":"Preterm Infant Resistome 1 — PretermInfantResistome2","text":"Preterm Infant Resistome II study profiled stool metagenome preterm infants (born < 33 weeks gestational age) throughout first 21 months life. Patients stratified antibiotic use hospitalization 41 preterm infants 17 antibiotic-naive, healthy early term late-preterm infants seen Washington University School Medicine St. Louis, MO, USA 437 stool samples; 'shotgun' metagenomic sequencing. Prospective cohort design.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Preterm Infant Resistome 1 — PretermInfantResistome2","text":"","code":"PretermInfantResistome2"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome2.html","id":"preterminfantresistome-","dir":"Reference","previous_headings":"","what":"PretermInfantResistome2","title":"Preterm Infant Resistome 1 — PretermInfantResistome2","text":"MbioDataset object 24 metadata variables, 427 shotgun stool samples. contains following collections:  \"Shotgun metagenomics: 4th level EC metagenome abundance data\"  \"Shotgun metagenomics: Metagenomeenzyme pathway abundance data\"  \"Shotgun metagenomics: Metagenomeenzyme pathway coverage data\"   \"Shotgun metagenomics: Genus\"  \"Shotgun metagenomics: Species\"  \"Shotgun metagenomics: Family\"  \"Shotgun metagenomics: Order\"  \"Shotgun metagenomics: Phylum\"  \"Shotgun metagenomics: Class\"   \"Shotgun metagenomics: Kingdom\"   \"Shotgun metagenomics: Normalized number taxon-specific sequence matches\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome2.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Preterm Infant Resistome 1 — PretermInfantResistome2","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_b9dc726b20/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/PretermInfantResistome2.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Preterm Infant Resistome 1 — PretermInfantResistome2","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/UgandaMaternal.html","id":null,"dir":"Reference","previous_headings":"","what":"Uganda Maternal — UgandaMaternal","title":"Uganda Maternal — UgandaMaternal","text":"Uganda Maternal microbiome study profled vaginal samples obtained Ugandan pregnant women active labor birth. Patients catergorizd intrapartum fever status 99 adult intrapartum women seen Mbarara (n=50) Mbale (n=49) Hospitals western eastern Uganda, respectively 99 vaginal swab samples; profiled using V1-V2 V3-V4 region 16S rRNA gene.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/UgandaMaternal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Uganda Maternal — UgandaMaternal","text":"","code":"UgandaMaternal"},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/UgandaMaternal.html","id":"ugandamaternal","dir":"Reference","previous_headings":"","what":"UgandaMaternal","title":"Uganda Maternal — UgandaMaternal","text":"MbioDataset object 11 metadata variables, 99 successful V1V2 assays 97 successful V3V4 assays. contains following collections:  \"16S V1V2 Order\"  \"16S V1V2 Genus\"  \"16S V1V2 Family\"  \"16S V1V2 Species\"  \"16S V1V2 Class\"  \"16S V1V2 Phylum\"  \"16S V1V2 Kingdom\"  \"16S V3V4 Order\"  \"16S V3V4 Genus\"  \"16S V3V4 Family\"  \"16S V3V4 Species\"  \"16S V3V4 Class\"  \"16S V3V4 Phylum\"  \"16S V3V4 Kingdom\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/UgandaMaternal.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Uganda Maternal — UgandaMaternal","text":"https://microbiomedb.org/mbio/app/workspace/analyses/DS_d3053dfc9c/new/download","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/UgandaMaternal.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Uganda Maternal — UgandaMaternal","text":"Website Release 32. (2023 May 30)","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/getCuratedDatasetNames.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Curated Data Set Names — getCuratedDatasetNames","title":"Get Curated Data Set Names — getCuratedDatasetNames","text":"Returns vector curated data set names 'microbiomeData' package. data MicrobiomeDB.org website can analyzed 'MicrobiomeDB' R package.","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/getCuratedDatasetNames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Curated Data Set Names — getCuratedDatasetNames","text":"","code":"getCuratedDatasetNames()"},{"path":"https://microbiomedb.github.io/microbiomeData/reference/getCuratedDatasetNames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Curated Data Set Names — getCuratedDatasetNames","text":"vector curated data set names","code":""},{"path":"https://microbiomedb.github.io/microbiomeData/reference/microbiomeData-package.html","id":null,"dir":"Reference","previous_headings":"","what":"microbiomeData: Curated Data from MicrobiomeDB.org — microbiomeData-package","title":"microbiomeData: Curated Data from MicrobiomeDB.org — microbiomeData-package","text":"R package containing curated datasets MicrobiomeDB.org.","code":""},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeData/reference/microbiomeData-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"microbiomeData: Curated Data from MicrobiomeDB.org — microbiomeData-package","text":"Maintainer: Danielle Callan dcallan@upenn.edu","code":""}]