bedGraphToBigWig

Roadmap Epigenomics — NIH Roadmap Epigenomics Mapping Consortium reference epigenomes spanning 111 primary human tissues and cell types. Provides ChIP-seq histone mark tracks (H3K4me1, H3K4me3, H3K27m

3 shared topics • 1 shared operation

wigToBigWig converts Wiggle (.wig) format files — fixedStep and variableStep — to bigWig binary format for genome browsers (UCSC, IGV, WashU Epigenome Browser). Essential for ChIP-seq, ATAC-seq, RNA-s

2 shared topics • 2 shared operations

Analyze bioinformatics sample metadata to auto-detect data modality, column semantics, and sequencing platform from CSV/TSV files, SRA RunTables, GEO Series Matrix files, and AnnData .obs exports. Inf

2 shared topics • 1 shared operation

Bowtie2 — ultrafast and memory-efficient short-read aligner using FM-index with gapped alignment and local alignment modes. Standard aligner for ChIP-seq, ATAC-seq, CUT&RUN, CUT&Tag, and general short

2 shared topics • 1 shared operation

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 • 1 shared operation