deploy: 2fee9ff

_sources/notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb

@@ -623,7 +623,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Below is a function that can be used to load specific genes from the from the full set of data in the WHB dataset. Adjust the chunk size down if you find your system still running out of memory. Additionally, reduce the number of genes if you still have issues. Note that the funciton can load either the raw expression data or the log2 data. The full code of this function can be found [here](https://github.com/AllenInstitute/abc_atlas_access/blob/4c4a7dfb124971b543de2cb737d059e7cabd620a/src/abc_atlas_access/abc_atlas_cache/anndata_utils.py#L9)"
+    "Below is a function that can be used to load specific genes from the from the full set of data in the WHB dataset. Adjust the chunk size down if you find your system still running out of memory. Additionally, reduce the number of genes if you still have issues. Note that the funciton can load either the raw expression data or the log2 data. The full code of this function can be found [here](https://github.com/AllenInstitute/abc_atlas_access/blob/7a53a08cff0f07e9b67911c0db04fa6932fa6e9d/src/abc_atlas_access/abc_atlas_cache/anndata_utils.py#L9)"
    ]
   },
   {

_sources/notebooks/getting_started.ipynb

@@ -105,7 +105,7 @@
     }
    ],
    "source": [
-    "pip install -U git+https://github.com/alleninstitute/abc_atlas_access@u/morriscb/updateJupyterBook"
+    "pip install -U git+https://github.com/alleninstitute/abc_atlas_access"
    ]
   },
   {

notebooks/general_accessing_10x_snRNASeq_tutorial.html

@@ -884,7 +884,7 @@ <h3>Loading specific genes from the data<a class="headerlink" href="#loading-spe
 </div>
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-<p>Below is a function that can be used to load specific genes from the from the full set of data in the WHB dataset. Adjust the chunk size down if you find your system still running out of memory. Additionally, reduce the number of genes if you still have issues. Note that the funciton can load either the raw expression data or the log2 data. The full code of this function can be found <a class="reference external" href="https://github.com/AllenInstitute/abc_atlas_access/blob/4c4a7dfb124971b543de2cb737d059e7cabd620a/src/abc_atlas_access/abc_atlas_cache/anndata_utils.py#L9">here</a></p>
+<p>Below is a function that can be used to load specific genes from the from the full set of data in the WHB dataset. Adjust the chunk size down if you find your system still running out of memory. Additionally, reduce the number of genes if you still have issues. Note that the funciton can load either the raw expression data or the log2 data. The full code of this function can be found <a class="reference external" href="https://github.com/AllenInstitute/abc_atlas_access/blob/7a53a08cff0f07e9b67911c0db04fa6932fa6e9d/src/abc_atlas_access/abc_atlas_cache/anndata_utils.py#L9">here</a></p>
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 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="o">?</span>get_gene_data

notebooks/getting_started.html

@@ -474,7 +474,7 @@ <h1>Getting started<a class="headerlink" href="#getting-started" title="Permalin
 <p>Below we install the python library we will be using throughout to this python enviroment.</p>
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-<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="o">-</span><span class="n">U</span> <span class="n">git</span><span class="o">+</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">alleninstitute</span><span class="o">/</span><span class="n">abc_atlas_access</span><span class="nd">@u</span><span class="o">/</span><span class="n">morriscb</span><span class="o">/</span><span class="n">updateJupyterBook</span>
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="o">-</span><span class="n">U</span> <span class="n">git</span><span class="o">+</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">alleninstitute</span><span class="o">/</span><span class="n">abc_atlas_access</span>
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