Merge pull request #408 from d3b-center/naqvia/update-readmes

readme updates

analyses/CLK1-splicing-impact-morpholino/README.md

@@ -43,8 +43,10 @@ bash run_module.sh
 │   ├── CCMA_crispr_genedependency_042024.csv
 │   ├── RBP_known.txt
 │   ├── base_excision_repair.txt
+│   ├── cancerGeneList.tsv
 │   ├── dna_repair_all.txt
 │   ├── epi_known.txt
+│   ├── genelistreference.txt
 │   ├── homologous_recombination.txt
 │   ├── mismatch_repair.txt
 │   ├── morpholno.merged.rmats.tsv
@@ -72,6 +74,7 @@ bash run_module.sh
 │   ├── dPSI_distr.pdf
 │   ├── des-dex-venn-func.pdf
 │   ├── des-dex-venn.pdf
+│   ├── ds-de-crispr-venn.pdf
 │   ├── gene-fam-DE-plot.pdf
 │   ├── gsva_heatmap_dna_repair.pdf
 │   ├── gsva_heatmap_dna_repair_de.pdf
@@ -94,9 +97,9 @@ bash run_module.sh
 │   ├── ctrl_vs_treated.de.formatted.tsv
 │   ├── ctrl_vs_treated.de.tsv
 │   ├── de_genes.tsv
+│   ├── dex-sign-goi.tsv
 │   ├── differential_splice_by_goi_category.tsv
 │   ├── ds-de-crispr-events.tsv
-│   ├── ds-de-crispr-venn.pdf
 │   ├── expr_collapsed_clk1_ctrl_morpho_dna_repair_gsva_scores.tsv
 │   ├── expr_collapsed_clk1_ctrl_morpho_hallmark_gsva_scores.tsv
 │   ├── expr_collapsed_clk1_ctrl_morpho_kegg_gsva_scores.tsv
@@ -129,4 +132,4 @@ bash run_module.sh
 │   ├── splicing_events.morpho.RI.intersectUnip.ggplot.txt
 │   └── splicing_events.morpho.SE.intersectUnip.ggplot.txt
 └── run_module.sh
-```
+```

analyses/cohort_summary/README.md

@@ -0,0 +1,32 @@
+# Cohort summary
+
+Module authors: Ammar Naqvi (@naqvia)
+
+The purpose of this module is to summarize cohort in our downstream analyses.
+
+## Usage
+<br>**Run shell script to make final tables to be used for plotting below**
+```
+bash run_module.sh
+```
+Input files (`data` folder):
+```
+histologies.tsv
+independent-specimens.rnaseqpanel.primary.tsv
+```
+
+## Folder content
+* `01-generate-cohort-summary-circos-plot.R` creates circos plot of cohort highlighting histology, CNS region and reported gender
+
+## Directory structure
+```
+.
+├── 01-generate-cohort-summary-circos-plot.R
+├── input
+│   └── plot-mapping.tsv
+├── plots
+│   └── cohort_circos.pdf
+└── results
+    ├── histologies-plot-group.tsv
+    └── plot_mapping.tsv
+```

analyses/histology-specific-splicing/README.md

@@ -21,18 +21,22 @@ independent-specimens.rnaseqpanel.primary-plus.tsv
 * `run_module.sh` shell script to pre-process histology file and run analysis
 * `01-generate_hist_spec_events_tab.pl` processes rMATs output and identifies unique splicing events if it is in 2% of the histology-specific cohort
 * `02-plot_histology-specific_splicing_events.R` takes result table frmo above and generates UpSetR plots for each splicing case
+* `03-plot-histology-specific-norm-events.R` computes and plots the average number of unique events per histology
 
 ## Directory structure
 ```
 .
 ├── 01-generate_hist_spec_events_tab.pl
 ├── 02-plot_histology-specific_splicing_events.R
+├── 03-plot-histology-specific-norm-events.R
+├── README.md
 ├── plots
+│   ├── avg-uniq-hits.pdf
 │   ├── upsetR_histology-specific.ei.pdf
 │   └── upsetR_histology-specific.es.pdf
 ├── results
+│   ├── recurrent_splice_events_by_histology.tsv
 │   ├── unique_events-ei.tsv
-│   ├── unique_events-es.tsv
-│   └── splicing_events.hist-labeled_list.thr2freq.txt
+│   └── unique_events-es.tsv
 └── run_module.sh
 ```

analyses/splicing_events_functional_sites/README.md

@@ -44,3 +44,33 @@ results/splicing_events.total.HGG.neg.intersectUnip.ggplot.txt
 * `03-format_for_ggplot.sh` formats and appends file into table for plotting
 * `04-plot_splicing_across_functional_sites.R` generates ggplot violin plots of average dPSI per event identidied overlapping a functional site, outputting to `plots/*png`
 * `05-plot-splice-patterns` generates plots for visualizing splicing event types into `plots` folder
+
+## Directory structure
+.
+├── 01-extract_recurrent_splicing_events_hgg.pl
+├── 02-run_bedtools_intersect.sh
+├── 02-run_bedtools_intersect.tmp.sh
+├── 03-format_for_ggplot.pl
+├── 04-plot_splicing_across_functional_sites.R
+├── 05-plot-splice-patterns.R
+├── README.md
+├── input
+│   ├── CLK1-rmats.tsv
+│   ├── gene_lists.tsv
+│   ├── unipDisulfBond.hg38.col.bed
+│   ├── unipDomain.hg38.col.bed
+│   ├── unipLocSignal.hg38.col.bed
+│   ├── unipMod.hg38.col.bed
+│   └── unipOther.hg38.col.bed
+├── plots
+│   ├── dPSI_across_functional_sites.HGG.pdf
+│   ├── dPSI_across_functional_sites_kinase.HGG.pdf
+│   ├── kinases-ora-plot.pdf
+│   └── splicing_pattern_plot.pdf
+├── results
+│   ├── kinases-functional_sites.tsv
+│   ├── splice_events.diff.SE.txt
+│   ├── splicing_events.SE.total.neg.intersectunip.ggplot.txt
+│   └── splicing_events.SE.total.pos.intersectunip.ggplot.txt
+├── run_module.sh
+└── scr

analyses/stranded-polyA-assessment/README.md

@@ -5,7 +5,7 @@ This module correlates polyA and stranded PSIs from patient samples known to hav
 ## Usage
 `bash run_module`
 
-## Folder content 
+## Folder content
 `01-plot-str-vs-polyA.Rmd` runs correlation analysis on samples with both stranded and polyA RNA-seq and generates scatter plots.
 
 ```
@@ -17,4 +17,14 @@ This module correlates polyA and stranded PSIs from patient samples known to hav
 │   ├── PT_RYMG3M91_polyA_v_stranded_psi.pdf
 │   └── PT_W5GP3F6B_polyA_v_stranded_psi.pdf
 └── run_module.sh
-```
+```
+
+## Directory structure
+.
+├── 01-plot-str-vs-polyA.Rmd
+├── 01-plot-str-vs-polyA.html
+├── README.md
+├── plots
+│   ├── PT_RYMG3M91_polyA_v_stranded_psi.pdf
+│   └── PT_W5GP3F6B_polyA_v_stranded_psi.pdf
+└── run_module.sh