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Use when working with DoRothEA or CollecTRI for transcription factor activity inference, gene regulatory network analysis, or regulon-based enrichment in single-cell or bulk RNA-seq data. DoRothEA pro
Use with AI
Install the MCP server or CLI to instantly fetch DoRothEA / CollecTRI documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/dorotheacollectri
bedGraphToBigWig converts bedGraph coverage files to bigWig binary format for genome browsers (UCSC, IGV, WashU Epigenome Browser). Essential for ChIP-seq, ATAC-seq, RNA-seq, and WGBS coverage tracks.
2 shared topics
deepTools — suite of Python tools for efficient analysis and visualization of high-throughput sequencing data including ChIP-seq, ATAC-seq, MNase-seq, and RNA-seq. BAM-to-bigWig conversion with normal
2 shared topics
Use when working with pybedtools — pybedtools — Python interface to BEDTools
2 shared topics
pygenometracks -- Python program and library for plotting publication-quality genome browser tracks. Generates highly customizable visualizations of bigwig, BED, GTF, bedgraph, Hi-C matrices, links/ar
2 shared topics
RASQUAL (Robust Allele Specific QUantification and quality controL) — joint QTL mapping tool that integrates total read counts and allele-specific reads for cis-regulatory variant discovery. Detects i
2 shared topics