HMMRATAC

TOBIAS — Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal. Python toolkit for differential transcription factor (TF) footprinting from ATAC-seq data. Corrects Tn5 insertio

3 shared topics

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 (

2 shared topics • 1 shared operation

nf-core/chipseq — Nextflow pipeline for comprehensive ChIP-seq analysis from raw reads through peak calling and differential analysis. Automates adapter trimming, multi-aligner support (BWA, Bowtie2,

2 shared topics • 1 shared operation

BEDTools — Swiss-army knife for genome arithmetic on genomic intervals. Provides intersect, merge, subtract, complement, closest, window, coverage, genomecov, slop, flank, sort, groupby, getfasta, mas

2 shared topics

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

2 shared topics