Merge main into wilms azimuth branch

.github/components/dictionary.txt

@@ -7,9 +7,11 @@ altExp
 anaplasia
 anaplastic
 aneuploid
+aneuploidy
 AnnData
 anonymize
 anonymized
+ARI
 astrocytes
 AUCell
 authenticator
@@ -23,8 +25,10 @@ bioinformatics
 blastema
 blastemal
 Bleijs
+Cao
 Carpentries
 CellAssign
+CELLxGENE
 chondrocytes
 chr
 CLI
@@ -44,6 +48,7 @@ Ctrl
 cxds
 demultiplexing
 dendogram
+derangements
 designee
 discoverable
 DM
@@ -53,6 +58,7 @@ Dockerfile
 docstring
 docstrings
 DOI
+dotplots
 doxxing
 dropdown
 ECM
@@ -61,7 +67,10 @@ endothelium
 enforceability
 Ensembl
 enure
+epithelia
+epithelialize
 erythematosus
+erythroid
 et
 ewings
 EWS-FLI1
@@ -75,12 +84,17 @@ GHAs
 GitHub
 GitKraken
 GitKraken's
+glial
+glioblastoma
 Goodspeed
 GPUs
 GTF
+Hafemeister
 Halbritter
+hematopoietic
 heterotypic
 histological
+histologies
 homotypic
 HPC
 IAM
@@ -95,6 +109,8 @@ Jaccard
 Jitter
 JSON
 Jupyter
+karyotyping
+leiden
 LGBTQ
 licensor
 licensor's
@@ -105,29 +121,40 @@ linter
 linter's
 linters
 lockfile
+Looney
 Louvain
 LSfR
 macOS
 macrophage
 md
 merchantability
 mesenchymal
+mesenchyme
 metacell
 metacells
+metanephric
+microenvironment
+microRNA
 Miniconda
 Miniforge
 misidentification
+monocyte
+monocytes
 MSC
 multifactor
 myeloid
 natively
 Nextflow
+nephroblastoma
+nephron
 nonconsensual
 octicons
 onboarded
+oncotarget
 openscpca
 OpenScPCA
 OpenScPCA's
+overclustered
 Panglao
 PanglaoDB
 PDX
@@ -139,14 +166,19 @@ Posit's
 PowerShell
 PR
 pre
+preprint
 PRs
+pseudobulk
 README
 redistribution
 redistributions
 renv
 repo
 reproducibility
 reproducibly
+ribosomal
+RNAseq
+rOpenScPCA
 RStudio
 RStudio's
 Rtools
@@ -166,7 +198,9 @@ SSO
 stroma
 stromal
 Stumptown
+subdiagnosis
 sublicensable
+subtypes
 symlink
 symlinked
 synched
@@ -175,12 +209,14 @@ Tirode
 trainings
 transferrable
 transphobic
+Treg
 triaged
 TSV
 UCell
 UMAP
 uncomment
 unhide
+uteric
 vCPU
 vCPUs
 Visser
@@ -193,3 +229,4 @@ Xcode
 YAML
 Zappia
 Zenodo
+Zhang

.github/workflows/docker_cell-type-wilms-tumor-14.yml

@@ -13,22 +13,22 @@ concurrency:
   cancel-in-progress: true
 
 on:
-  # pull_request:
-  #   branches:
-  #     - main
-  #   paths:
-  #     - "analyses/cell-type-wilms-tumor-14/Dockerfile"
-  #     - "analyses/cell-type-wilms-tumor-14/.dockerignore"
-  #     - "analyses/cell-type-wilms-tumor-14/renv.lock"
-  #     - "analyses/cell-type-wilms-tumor-14/conda-lock.yml"
-  # push:
-  #   branches:
-  #     - main
-  #   paths:
-  #     - "analyses/cell-type-wilms-tumor-14/Dockerfile"
-  #     - "analyses/cell-type-wilms-tumor-14/.dockerignore"
-  #     - "analyses/cell-type-wilms-tumor-14/renv.lock"
-  #     - "analyses/cell-type-wilms-tumor-14/conda-lock.yml"
+  pull_request:
+    branches:
+      - main
+    paths:
+      - "analyses/cell-type-wilms-tumor-14/Dockerfile"
+      - "analyses/cell-type-wilms-tumor-14/.dockerignore"
+      - "analyses/cell-type-wilms-tumor-14/renv.lock"
+      - "analyses/cell-type-wilms-tumor-14/conda-lock.yml"
+  push:
+    branches:
+      - main
+    paths:
+      - "analyses/cell-type-wilms-tumor-14/Dockerfile"
+      - "analyses/cell-type-wilms-tumor-14/.dockerignore"
+      - "analyses/cell-type-wilms-tumor-14/renv.lock"
+      - "analyses/cell-type-wilms-tumor-14/conda-lock.yml"
   workflow_dispatch:
     inputs:
       push-ecr:

.github/workflows/run_cell-type-nonETP-ALL-03.yml

@@ -89,4 +89,5 @@ jobs:
           # run module script(s) here
           Rscript scripts/00-01_processing_rds.R
           Rscript scripts/02-03_annotation.R
-          Rscript scripts/multipanel_plot.R
+          Rscript scripts/04_multipanel_plot.R
+          Rscript scripts/05_cluster_evaluation.R

.github/workflows/run_cell-type-wilms-tumor-14.yml

@@ -64,6 +64,11 @@ jobs:
         with:
           working-directory: ${{ env.MODULE_PATH }}
 
+      - name: Initialize zellkonverter environment
+        run: |
+          cd ${MODULE_PATH}
+          Rscript -e "proc <- basilisk::basiliskStart(env = zellkonverter::zellkonverterAnnDataEnv(), testload = 'anndata'); basilisk::basiliskStop(proc)"
+
       # Update this step as needed to download the desired data
       - name: Download test data and results
         run: |

analyses/cell-type-dsrct/.Rprofile

@@ -0,0 +1,4 @@
+# Don't activate renv in an OpenScPCA docker image
+if(Sys.getenv('OPENSCPCA_DOCKER') != 'TRUE'){
+  source('renv/activate.R')
+}

analyses/cell-type-dsrct/cell-type-dsrct.Rproj

@@ -0,0 +1,13 @@
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX