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DepMap/CCLE tools for cancer dependency mapping and cell line omics analysis. Access CRISPR gene effect scores (Chronos/CERES), RNAi dependency data, gene expression (TPM), copy number alterations, so
Use with AI
Install the MCP server or CLI to instantly fetch DepMap/CCLE Tools documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/depmapccle-tools
Bismark — bisulfite-seq alignment and methylation calling toolkit. Maps bisulfite-treated reads to a reference genome using Bowtie 2, HISAT2, or minimap2, performs cytosine methylation calls in CpG/CH
1 shared topic • 1 shared operation
BWA-MEM2 — accelerated Burrows-Wheeler Aligner for mapping short DNA reads to reference genomes. Use when aligning Illumina WGS, WES, targeted panel, ChIP-seq, or ATAC-seq FASTQ reads. Drop-in replace
1 shared topic • 1 shared operation
Ensembl Database — EMBL-EBI's comprehensive genome annotation database covering 300+ species with gene models, variants, regulatory features, and comparative genomics. Query via REST API at rest.ensem
1 shared topic • 1 shared operation
GATK HaplotypeCaller — germline short variant caller using localized de novo assembly of haplotypes. Calls SNPs and indels from BAM/CRAM alignment files, producing VCF or gVCF output. Supports single-
1 shared topic • 1 shared operation
OrthoFinder — fast, accurate ortholog inference for comparative genomics. Identifies orthogroups, orthologs, gene trees, rooted species trees, and gene duplication events from protein or nucleotide se
1 shared topic • 1 shared operation