MEME Suite

MACS2/MACS3 — Model-based Analysis of ChIP-Seq for identifying transcription factor binding sites and histone modification enrichment from ChIP-seq, ATAC-seq, and CUT&Tag data. Provides peak calling (

3 shared topics

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 • 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

MEME Suite — comprehensive motif analysis toolkit for DNA, RNA, and protein sequences. Provides de novo motif discovery (MEME, STREME), motif scanning (FIMO), motif comparison (TOMTOM), motif enrichme

2 shared topics • 1 shared operation

MOABS (Model Based Analysis of Bisulfite Sequencing) — epigenomics toolkit for DNA methylation calling and differential methylation analysis from WGBS and RRBS experiments. Core tools: mcall (CpG meth

2 shared topics • 1 shared operation