Merge pull request #504 from AlexsLemonade/auto_render_live

GHA: Automated live (rendered) versions of the notebooks
AlexsLemonade · Sep 14, 2021 · 3763d14 · 3763d14
2 parents a8a6a3d + f495225
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diff --git a/RNA-seq/02-gastric_cancer_tximeta.nb.html b/RNA-seq/02-gastric_cancer_tximeta.nb.html
@@ -644,12 +644,12 @@ <h2>Import expression data with <code>tximeta</code></h2>
 <!-- rnb-message-begin eyJkYXRhIjoicmVhZGluZyBpbiBmaWxlcyB3aXRoIHJlYWRfdHN2XG4ifQ== -->
 <pre><code>reading in files with read_tsv</code></pre>
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 <pre><code>1 2 3 4 5 6 7 8 
 found matching transcriptome:
 [ Ensembl - Homo sapiens - release 95 ]
 useHub=TRUE: checking for EnsDb via &#39;AnnotationHub&#39;
-using temporary cache /tmp/RtmpHVYse0/BiocFileCache
+using temporary cache /tmp/RtmpnKSXlg/BiocFileCache
 snapshotDate(): 2020-10-27
 found matching EnsDb via &#39;AnnotationHub&#39;
 downloading 1 resources
@@ -671,8 +671,8 @@ <h2>Summarize to gene</h2>
 <pre class="r"><code># Summarize to the gene level
 gene_summarized &lt;- summarizeToGene(txi_data) </code></pre>
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-<pre><code>loading existing EnsDb created: 2021-06-22 14:34:26</code></pre>
+<!-- rnb-message-begin eyJkYXRhIjoibG9hZGluZyBleGlzdGluZyBFbnNEYiBjcmVhdGVkOiAyMDIxLTA5LTE0IDE1OjAzOjU5XG4ifQ== -->
+<pre><code>loading existing EnsDb created: 2021-09-14 15:03:59</code></pre>
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 <pre><code>obtaining transcript-to-gene mapping from database</code></pre>

diff --git a/RNA-seq/03-gastric_cancer_exploratory-live.Rmd b/RNA-seq/03-gastric_cancer_exploratory-live.Rmd
@@ -50,11 +50,6 @@ txi_dir <- file.path(data_dir, "txi")
 txi_file <- file.path(txi_dir, "gastric-cancer_tximeta.RDS")
 ```
 
-```{r metadata-file}
-# sample metadata file
-meta_file <- file.path(data_dir, "gastric-cancer_metadata.tsv")
-```
-
 We'll create a directory to hold our plots.
 
 ```{r plots-dir, live = TRUE}

diff --git a/RNA-seq/03-gastric_cancer_exploratory.nb.html b/RNA-seq/03-gastric_cancer_exploratory.nb.html
diff --git a/scRNA-seq/02-filtering_scRNA.nb.html b/scRNA-seq/02-filtering_scRNA.nb.html
diff --git a/scRNA-seq/03-normalizing_scRNA.nb.html b/scRNA-seq/03-normalizing_scRNA.nb.html
diff --git a/scRNA-seq/07-gene_set_enrichment_analysis-live.Rmd b/scRNA-seq/07-gene_set_enrichment_analysis-live.Rmd
@@ -95,7 +95,7 @@ We'll save our table of GSEA results as a TSV.
 
 ```{r output_files}
 output_file <- file.path(results_dir,
-                         "cluster01_hallmarks_gsea_results.tsv")
+                         "cluster01_immunologic_gsea_results.tsv")
 ```
 
 ## Gene sets

diff --git a/scRNA-seq/07-gene_set_enrichment_analysis.nb.html b/scRNA-seq/07-gene_set_enrichment_analysis.nb.html