ChromHMM

AlleleSeq — pipeline for detecting allele-specific expression (ASE) and allele-specific binding (ASB) from RNA-seq and ChIP-seq data at heterozygous SNP positions. Constructs a personal diploid genome

2 shared topics • 1 shared operation

BaalChIP — Bioconductor R package for detecting allele-specific binding (ASB) in ChIP-seq data. Identifies allelic imbalance at heterozygous SNPs using a Bayesian statistical framework with logistic r

2 shared topics • 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

2 shared topics • 1 shared operation

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

2 shared topics • 1 shared operation

WASP (Weight And SNP-based Pipeline) corrects allele-specific mapping bias in RNA-seq and ChIP-seq by SNP-masking reads that overlap heterozygous variants, remapping them, and filtering those that shi

2 shared topics • 1 shared operation