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macs2

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nf-core /chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.

workflow pipeline nextflow chip chip-seq macs2 nf-core chromatin-immunoprecipitation peak-calling

UpdatedMar 12, 2025
Nextflow

ay-lab /ATACProc

ATAC-seq processing pipeline

atac-seq qc macs2 atacseqqc

UpdatedApr 8, 2022
Shell

ay-lab /ChIPLine

ChIP-seq analysis pipeline

chip-seq qc idr macs2

UpdatedAug 15, 2024
Shell

HuntsmanCancerInstitute /MultiRepMacsChIPSeq

Multiple-replica multiple-condition Macs2 ChIPSeq wrapper

chip-seq atac-seq chromatin macs2 peak-calling

UpdatedJan 30, 2025
Perl

skchronicles /PeakCalling

Benchmarking ChIP-seq peak callers

music gem chip-seq sicer macs2 peak-analysis peak-calling broad-peaks narrow-peaks dfilter pepr

UpdatedDec 11, 2018
Python

uhkniazi /dismiss

DISMISS is an R script, which as an additional step in MeDIP-Seq data analysis workflow, enables the allocation of strands to methylated DNA regions. It does this by analyzing the proportions of first mate reads aligning to the methylated locus from the plus and minus strands.

methylation epigenetics macs2 medip medip-seq

UpdatedMay 13, 2016
R

jianhong /genomictools

docker file for genomic tools

rna-seq bioinformatics-pipeline chip-seq salmon kallisto bwa sleuth macs2 tximport

UpdatedJul 25, 2024
Dockerfile

sebastian-gregoricchio /SPACCa

Snakemake Pipeline for the Analyses of ChIP-seq data in Cancer samples

somatic-variants mutation gatk mutations chip-seq somatic-mutations normalization mutation-analysis copynumber macs chip-seq-callers macs2 chipseq somatic-indels gatk4 chip-seq-data chip-seq-analysis chip-seq-peaks somatic-variant

UpdatedOct 18, 2024
Python

stjude-biohackathon /peakPeekeR

Peak calling optimization via real time results assessment and interactive parameter adjustment.

shiny chip-seq atac-seq macs macs2 peak-calling cutandrun cutandtag genrich peak-callers sicer2

UpdatedApr 29, 2022
R

OrangePomeranian /ChiP-seq

This project explores the PBRM1-PIAS1 interaction in epithelial differentiation through ChIP-seq analysis, highlighting EZH2's role and implications for cholesterol biosynthesis in cellular processes.

bioinformatics bowtie2 macs2 chip-seq-analysis epithelial-tissue-differentiation

UpdatedFeb 9, 2024
Jupyter Notebook

elizabethpermina /ChIP-Seq-Otago-2017

chip-seq workshop-materials macs2

UpdatedDec 4, 2017

metamaden /seq_answers

Sequencing data preprocessing

mapping ngs sequencing entrez bigwig chip-seq peak-caller wiggle galaxy-project fastq bedtools ncbi samtools sra ucsc-browser bowtie2 chip-seq-pipelines galaxy-server macs2 bedfile

UpdatedJun 18, 2018
R

hisplan /docker-macs2

Dockerized MACS2

UpdatedJan 31, 2020
Shell

monnieb92 /PROseq_Intron_Intergenic_Enhancers

A pipeline to call intron and intergenic eRNAs from PRO-seq Data

homer featurecounts macs2 pro-seq intronic ernas nrsa

UpdatedFeb 19, 2024
Shell

CCBR /ASPEN

CCBR pipeline for preliminary QC, peak calling, differential chromatin accessibility analysis with ATACseq datasets 🌲

multiqc ngs-pipeline macs2 atac-seq-pipeline genrich

UpdatedFeb 28, 2025
Shell

tdayris /fair_macs2_calling

Snakemake workflow used to call peaks with Macs2

snakemake sambamba homer bowtie2 macs2 snakemake-workflow snakemake-wrappers

UpdatedMar 7, 2025
Python

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