mdhewei/bioinfor-claw/depmap-analysis-for-gene

Name: depmap-analysis-for-gene
Author: mdhewei

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mdhewei/bioinfor-claw
gene-centered-analysis/depmap-analysis-for-gene/SKILL.md
Updated 25 Oct 2026
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DepMap analysis for a gene across CANCER CELL LINES (NOT patient samples). Modules: expression, mutation, copy number, essentiality. Data is streamed directly from the DepMap API — no full dataset download needed. Also includes standalone co-expression (depmap_coexpression.py) and co-essentiality (depmap_coessentiality.py) scripts for cell-line correlations. For patient/tumor co-expression use coexpression-for-gene (TCGA/GTEx) instead.

Install

npx vskill@latest install mdhewei/bioinfor-claw/depmap-analysis-for-gene

SKILL.md

DepMap Analysis for Gene

Purpose

Analyze a single gene in DepMap across cancer cell lines.

The main script streams data directly from the DepMap download API and extracts ONLY the target gene's column. It never downloads or loads multi-GB whole-genome matrices into memory.

Supported modules (main script):

expression
mutation
copy_number
essentiality

Co-expression and co-essentiality require full matrices and use standalone scripts (see below).

Inputs

Required

--gene: Gene symbol, e.g. TP53
--outdir: Output directory

Module selection

--modules: Comma-separated list. Choices: expression, mutation, copy_number, essentiality, full. Default: full.

Examples:

--modules expression
--modules mutation,copy_number
--modules full

Analysis options

--top-n: Top rows to report (default: 20)
--amp-threshold: Copy number amplification threshold (default: 1.0)
--del-threshold: Copy number deletion threshold (default: -1.0)
--essential-threshold: Essentiality cutoff (default: -0.5)

IMPORTANT: No data file arguments needed

The script streams directly from DepMap URLs. Do NOT pass --expression-file, --mutation-file, --copy-number-file, --essentiality-file, or --metadata-file. These legacy flags are accepted but ignored.

Do NOT call depmap-download-data or depmap_downloader.py before running this script. The script handles its own data fetching.

Command template

bash

python scripts/depmap_analysis_for_gene.py --gene <GENE> --modules <MODULES> --outdir <OUTDIR> [--top-n N] [--amp-threshold X] [--del-threshold X] [--essential-threshold X]

Example commands

Expression only:

bash

python scripts/depmap_analysis_for_gene.py --gene TP53 --modules expression --outdir <OUTDIR>

Mutation + copy number:

bash

python scripts/depmap_analysis_for_gene.py --gene BRCA1 --modules mutation,copy_number --outdir <OUTDIR>

Full analysis:

bash

python scripts/depmap_analysis_for_gene.py --gene KRAS --modules full --outdir <OUTDIR>

Parameter decision guide

Signal in user request	Parameter to set
"expression across cell lines"	`--modules expression`
"mutation landscape"	`--modules mutation`
"copy number / amplification / deletion"	`--modules copy_number`
"essential? dependency? CRISPR screen?"	`--modules essentiality`
"what genes are co-expressed with X?"	MUST use standalone script `depmap_coexpression.py`
"what genes are co-essential with X?"	MUST use standalone script `depmap_coessentiality.py`
"co-expression in TCGA / patient samples"	Wrong skill! Use `coexpression-for-gene`
"full profile" or no specific module	`--modules full`

Outputs

Always

gene_depmap_summary.tsv
summary.txt

Expression

<GENE>.expression_top_cell_lines.tsv
<GENE>.expression_lineage_summary.tsv
<GENE>.expression_barplot.png / .pdf

Mutation

<GENE>.mutations.tsv
<GENE>.mutation_type_summary.tsv
<GENE>.mutation_protein_summary.tsv

Copy number

<GENE>.copy_number.tsv
<GENE>.copy_number_top_amplified.tsv
<GENE>.copy_number_top_deleted.tsv
<GENE>.copy_number_lineage_summary.tsv
<GENE>.copy_number_amplified_barplot.png / .pdf

Essentiality

<GENE>.essentiality.tsv
<GENE>.essentiality_top_cell_lines.tsv
<GENE>.essentiality_lineage_summary.tsv
<GENE>.essentiality_barplot.png / .pdf

Standalone co-expression / co-essentiality scripts

These require the full expression/essentiality matrix and produce richer outputs (barplot, network, FDR table).

DepMap co-expression

bash

python scripts/depmap_coexpression.py \
    --gene TP53 \
    --method pearson \
    --top-n 30 \
    --fdr-cutoff 0.05

DepMap co-essentiality

bash

python scripts/depmap_coessentiality.py \
    --gene TP53 \
    --method pearson \
    --top-n 30 \
    --fdr-cutoff 0.05

For co-expression/co-essentiality: do NOT include --expression-file or --essentiality-file in EXEC_ARGS. The server auto-locates cached DepMap data and injects the correct paths.

Failure conditions

Fail clearly if:

--gene is missing
--outdir is missing
the gene cannot be found in a DepMap dataset
network access to DepMap API fails

Security

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Source

SKILL.md in the repositoryCheckinggene-centered-analysis/depmap-analysis-for-gene/SKILL.md

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