Merge pull request #481 from d3b-center/archive-modules

update readmes for deprecated modules, remove unused modules
d3b-center · Dec 11, 2023 · 3cf1e3a · 3cf1e3a
2 parents 4802aa0 + 7402380
commit 3cf1e3a
Show file tree

Hide file tree

Showing 88 changed files with 170 additions and 10,765 deletions.
diff --git a/README.md b/README.md
diff --git a/analyses/README.md b/analyses/README.md
diff --git a/analyses/cnv-comparison/01-cnv-comparison-plotting.Rmd b/analyses/cnv-comparison/01-cnv-comparison-plotting.Rmd
diff --git a/analyses/cnv-comparison/01-cnv-comparison-plotting.nb.html b/analyses/cnv-comparison/01-cnv-comparison-plotting.nb.html
diff --git a/analyses/cnv-comparison/README.md b/analyses/cnv-comparison/README.md
diff --git a/analyses/cnv-comparison/plots/compare_cnv_output_barplot_aberration.pdf b/analyses/cnv-comparison/plots/compare_cnv_output_barplot_aberration.pdf
diff --git a/analyses/cnv-comparison/plots/compare_cnv_output_barplot_histology.pdf b/analyses/cnv-comparison/plots/compare_cnv_output_barplot_histology.pdf
diff --git a/analyses/cnv-comparison/plots/compare_cnv_output_frequency.pdf b/analyses/cnv-comparison/plots/compare_cnv_output_frequency.pdf
diff --git a/analyses/cnv-comparison/plots/compare_cnv_output_proportion.pdf b/analyses/cnv-comparison/plots/compare_cnv_output_proportion.pdf
diff --git a/analyses/cnv-comparison/plots/compare_cnv_output_violin_plot.pdf b/analyses/cnv-comparison/plots/compare_cnv_output_violin_plot.pdf
diff --git a/analyses/cnv-comparison/util/cnv-comparison-functions.R b/analyses/cnv-comparison/util/cnv-comparison-functions.R
diff --git a/analyses/cnv-frequencies/README.md b/analyses/cnv-frequencies/README.md
@@ -1,4 +1,5 @@
 ## Annotate CNV table with mutation frequencies
+This analysis is DEPRECATED and was last run with OpenPedCan data release `v12`.
 
 Adapted from [snv-frequencies](https://github.com/logstar/OpenPedCan-analysis/tree/snv-freq/analyses/snv-frequencies)
 **Module author:** Yuanchao Zhang ([@logstar](https://github.com/logstar))

diff --git a/analyses/collapse-rnaseq/README.md b/analyses/collapse-rnaseq/README.md
@@ -1,4 +1,6 @@
 ## Collapse RNA-seq matrices
+This analysis is DEPRECATED in that it was last run in the repo with OpenPBTA data release `v23`.
+This analysis is now run upstream.
 
 Many downstream modules require RNA-seq data that have gene symbols as gene identifiers.
 Multiple Ensembl gene identifiers map to the same gene symbol in a small proportion of cases.