dataset: DepMap

.github/workflows/publish.yml

@@ -57,11 +57,11 @@ jobs:
       - name: Run Snakemake workflow for DMMMs
         shell: bash --login {0}
         run: snakemake --cores 4 --configfile configs/dmmm.yaml --show-failed-logs -s spras/Snakefile
-      # - name: Run Snakemake workflow for PRAs
       #   shell: bash --login {0}
       #   run: snakemake --cores 1 --configfile configs/pra.yaml --show-failed-logs -s spras/Snakefile
       - name: Setup PNPM
         # TODO: re-enable PRAs once RN/synthetic data PRs are merged.
+        # - name: Run Snakemake workflow for PRAs
         uses: pnpm/action-setup@v4
         with:
           version: 10

datasets/depmap/.gitignore

@@ -0,0 +1,2 @@
+raw
+processed

datasets/depmap/README.md

@@ -8,21 +8,29 @@ You can read more DepMap and the projects included here: https://www.broadinstit
 You can visit the DepMap all data downloads portal at: https://depmap.org/portal/data_page/?tab=allData 
 Download the following datasets under the primary files section and move them to the raw folder, the dataset descriptions from the website is also included : 
 
+Currently used files: 
 
-- OmicsProfiles.csv: Omics metadata and ID mapping information for files indexed by Profile ID.This dataset is used for mapping cell line names to DepMap model IDs as a basis for data processing. (file URL: https://depmap.org/portal/data_page/?tab=allData&releasename=DepMap%20Public%2025Q2&filename=OmicsProfiles.csv) 
-- CRISPRGeneDependency.csv: Gene dependency probability estimates for all models in the integrated gene effect.
+- 'OmicsProfiles.csv': Omics metadata and ID mapping information for files indexed by Profile ID.This dataset is used for mapping cell line names to DepMap model IDs as a basis for data processing. (file URL: https://depmap.org/portal/data_page/?tab=allData&releasename=DepMap%20Public%2025Q2&filename=OmicsProfiles.csv) 
+- 'CRISPRGeneDependency.csv': Gene dependency probability estimates for all models in the integrated gene effect.
 This dataset is used to identify gold standard genes in each cell line, a dependency probability cutoff of 0.5 is currently used to get the genes with considerable impact on the cell line. (file URL: https://depmap.org/portal/data_page/?tab=allData&releasename=DepMap%20Public%2025Q2&filename=CRISPRGeneDependency.csv) 
-- OmicsCNGeneWGS.csv: Gene-level copy number data inferred from WGS data only.Additional copy number datasets are available for download as part of the full DepMap Data Release.(file URL: https://depmap.org/portal/data_page/?tab=allData&releasename=DepMap%20Public%2025Q2&filename=OmicsCNGeneWGS.csv) 
-- OmicsSomaticMutationsMatrixDamaging.csv: Genotyped matrix determining for each cell line whether each gene has at least one damaging mutation. A variant is considered a damaging mutation if LikelyLoF == True. (0 == no mutation; If there is one or more damaging mutations in the same gene for the same cell line, the allele frequencies are summed, and if the sum is greater than 0.95, a value of 2 is assigned and if not, a value of 1 is assigned.). This dataset is used to prepare the input prize file. (file URL: https://depmap.org/portal/data_page/?tab=allData&releasename=DepMap%20Public%2025Q2&filename=OmicsSomaticMutationsMatrixDamaging.csv) 
-- OmicsExpressionProteinCodingGenesTPMLogp1.csv:Model-level TPMs derived from Salmon v1.10.0 (Patro et al 2017) Rows: Model IDs Columns: Gene names. (file URL: https://depmap.org/portal/data_page/?tab=allData&releasename=DepMap%20Public%2025Q2&filename=OmicsExpressionProteinCodingGenesTPMLogp1.csv) 
+- 'OmicsSomaticMutationsMatrixDamaging.csv': Genotyped matrix determining for each cell line whether each gene has at least one damaging mutation. A variant is considered a damaging mutation if LikelyLoF == True. (0 == no mutation; If there is one or more damaging mutations in the same gene for the same cell line, the allele frequencies are summed, and if the sum is greater than 0.95, a value of 2 is assigned and if not, a value of 1 is assigned.). This dataset is used to prepare the input prize file. (file URL: https://depmap.org/portal/data_page/?tab=allData&releasename=DepMap%20Public%2025Q2&filename=OmicsSomaticMutationsMatrixDamaging.csv) 
+
+Future extention files: 
+
+- 'OmicsExpressionProteinCodingGenesTPMLogp1.csv':Model-level TPMs derived from Salmon v1.10.0 (Patro et al 2017) Rows: Model IDs Columns: Gene names. (file URL: https://depmap.org/portal/data_page/?tab=allData&releasename=DepMap%20Public%2025Q2&filename=OmicsExpressionProteinCodingGenesTPMLogp1.csv) 
+- 'OmicsCNGeneWGS.csv': Gene-level copy number data inferred from WGS data only. Additional copy number datasets are available for download as part of the full DepMap Data Release.(file URL: https://depmap.org/portal/data_page/?tab=allData&releasename=DepMap%20Public%2025Q2&filename=OmicsCNGeneWGS.csv) 
+
 
 ## scripts
-Currently only the Jupyter notebook file I used to analyze dependency data and do the data processing locally to get the input prize file and gold standards. Should be reproducible for any cell line name, but is not yet organized or refined for GitHub.  
+Currently only the Jupyter notebook file used to analyze dependency data and do the data processing locally to get the input prize file and gold standards. Should be reproducible for any cell line name, but is not yet organized or refined for GitHub. 
+'OmicsProfiles.csv' used for mapping cell line names to DepMap model IDs. 
+'OmicsSomaticMutationsMatrixDamaging.csv' used for preparing prize input file. 
+'CRISPRGeneDependency.csv' used for preparing gold standard output.  
 
 ## processed data 
 Files used for Uniprot ID mapping: 
-- Gene symbols parsed 
-- Gene symbols mapped to Uniprot IDs 
+- 'DamamingMutationsGeneSymbols_20250718.csv': Gene symbols parsed from gene columns in 'OmicsSomaticMutationsMatrixDamaging.csv' on the date described
+- 'DamagingMutations_idMapping_20250718.tsv': Gene symbols from 'DamamingMutationsGeneSymbols_20250718.csv' mapped to Uniprot IDs using Uniprot Web Service on the date described
 - folder of processed data for an attempt to do UniProt mapping with the gene index numbers instead, got stuck due to duplicate matches for the same gene number, a future step could be referring to the original mutations file(OmicsSomaticMutations.csv on DepMap, URL: https://depmap.org/portal/data_page/?tab=allData&releasename=DepMap%20Public%2025Q2&filename=OmicsSomaticMutations.csv) for gene numbers with duplicate matches and do exact matches by seeing where the mutation is located and get more accurate mappings. 
 
 Started processing with the FADU cell line: 
@@ -31,4 +39,8 @@ Started processing with the FADU cell line:
 
 ## config 
 Example Config file used to get preliminary results on OmicsIntegrator1 and 2 following the EGFR dataset example. Will test out more parameters and update. 
+The input edge file for the background network can be obtained from the SPRAS repo 'input/phosphosite-irefindex13.0-uniprot.txt' 
 
+## Release Citation 
+For DepMap Release data, including CRISPR Screens, PRISM Drug Screens, Copy Number, Mutation, Expression, and Fusions:
+DepMap, Broad (2025). DepMap Public 25Q2. Dataset. depmap.org

datasets/depmap/config/cellline_fadu.yaml

@@ -6,22 +6,21 @@ hash_length: 7
 singularity: false
 
 algorithms:
-  -
-    name: pathlinker
+  - name: pathlinker
     params:
       include: false
       run1:
         k:
           - 10
           - 20
-  -
-    name: omicsintegrator1
+  - name: omicsintegrator1
     params:
       include: true
       run1:
         b:
-          - 0.55
           - 2
+          - 4
+          - 7
           - 10
         d:
           - 10
@@ -31,11 +30,12 @@ algorithms:
           - 0.01
         w:
           - 0.1
+          - 0.2
         mu:
           - 0.008
+          - 0.01
         dummy_mode: ["terminal"]
-  -
-    name: omicsintegrator2
+  - name: omicsintegrator2
     params:
       include: true
       run1:
@@ -48,8 +48,7 @@ algorithms:
           - 2
         g:
           - 3
-  -
-    name: meo
+  - name: meo
     params:
       include: false
       run1:
@@ -59,8 +58,7 @@ algorithms:
           - 3
         rand_restarts:
           - 10
-  -
-    name: domino
+  - name: domino
     params:
       include: false
       run1:
@@ -69,8 +67,7 @@ algorithms:
         module_threshold:
           - 0.05
 datasets:
-  -
-    data_dir: input
+  - data_dir: input
     edge_files:
       - phosphosite-irefindex13.0-uniprot.txt
     label: cellline