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chip-seq

Here are 70 public repositories matching this topic...

crazyhottommy / ChIP-seq-analysis

ChIP-seq analysis notes from Ming Tang

chip-seq histone-modifications transcription-factor-binding

Updated Aug 5, 2024
Python

macs3-project / MACS

MACS -- Model-based Analysis of ChIP-Seq

python dnase-seq chip-seq peak-caller atac-seq poisson-equation macs

Updated Nov 27, 2025
Python

deeptools / deepTools

Tools to process and analyze deep sequencing data.

python bioinformatics rna-seq genomics ngs chip-seq

Updated Jul 23, 2025
Python

maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data

workflow rna-seq snakemake ngs hi-c chip-seq atac-seq bisulfite-sequencing

Updated Dec 18, 2025
Python

seq2science

vanheeringen-lab / seq2science

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

bioinformatics rna-seq snakemake pipeline reproducible-research ngs bioinformatics-pipeline chip-seq atac-seq workflows fastq sra

Updated Nov 22, 2025
Python

crazyhottommy / pyflow-ChIPseq

a snakemake pipeline to process ChIP-seq files from GEO or in-house

python snakemake chip-seq

Updated Jan 1, 2026
Python

harbourlab / SparK

Publication quality NGS track plotting

rna-seq ngs plotting chip-seq igv ngs-analysis bedgraph-files

Updated Oct 10, 2025
Python

CostaLab / reg-gen

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

bioinformatics dnase-seq genomics ngs motif chip-seq atac-seq motif-analysis footprinting differential-peak-calling

Updated Nov 3, 2025
Python

epigen / enrichment_analysis

A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.

visualization workflow bioinformatics gene-sets rna-seq snakemake pipeline chip-seq atac-seq gene-set-enrichment enrichment-analysis genomic-regions biomedical-data-science motif-enrichment-analysis

Updated Sep 24, 2025
Python

dputhier / pygtftk

A python package and a set of shell commands to handle GTF files

bioinformatics gene rna-seq genomics cds ngs tts transcript bigwig chip-seq gtf bed exon tss dna-sequences genomic intron splicing

Updated Dec 18, 2025
Python

biocore-ntnu / epic

(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER

bioinformatics sicer-algorithm chip-seq peak-caller sicer chip-seq-callers

Updated Nov 21, 2018
Python

maxATAC

MiraldiLab / maxATAC

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks

chip-seq deeplearning atac-seq transcription-factor-binding genome-analysis maxatac

Updated Nov 21, 2025
Python

shao-lab / MAnorm

A robust model for quantitative comparison of ChIP-Seq data sets.

bioinformatics ngs chip-seq differential-expression normalization

Updated May 18, 2020
Python

TheJacksonLaboratory / pyBedGraph

A Python package for fast operations on 1-dimensional genomic signal tracks

bioinformatics chip-seq atac-seq bedgraph bedgraph-files

Updated Apr 3, 2020
Python

epigen / open_pipelines

Pipelines for NGS data preprocessing by the Bock lab and friends

bioinformatics rna-seq pipeline chip-seq atac-seq looper ngs-pipeline pypiper

Updated Aug 29, 2022
Python

odb9402 / CNNPeaks

The ChIP-Seq peak calling algorithm using convolution neural networks

bioinformatics tensorflow gpu docker-image chip-seq atac-seq nvidia-docker convolutional-neural-network samtools cnn-model ngs-analysis peak-calling progressbar2

Updated Jan 18, 2021
Python

DavideBrex / SpikeFlow

Pipeline to analyse ChIP-Rx data, i.e ChIP-Seq with reference exogenous genome spike-in normalization

bioinformatics snakemake bioinformatics-pipeline chip-seq snakemake-workflows normalisation spike-ins

Updated Sep 18, 2025
Python

afrendeiro / toolkit

A toolkit for NGS analysis with Python

bioinformatics rna-seq ngs project-management chip-seq atac-seq looper ngs-analysis pypiper

Updated Jan 18, 2023
Python

tushiqi / MAnorm2_utils

To pre-process a set of ChIP-seq samples and coordinate with MAnorm2 for differential analysis

python-library chip-seq normalization

Updated Apr 2, 2019
Python

biomedicalinformaticsgroup / Sargasso

Sargasso disambiguates mixed-species high-throughput sequencing data.

bioinformatics rna-seq chip-seq atac-seq high-throughput-sequencing

Updated Feb 6, 2024
Python

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