ChIP-seq peak-calling, QC and differential analysis pipeline.
☆230Nov 21, 2025Updated 3 months ago
Alternatives and similar repositories for chipseq
Users that are interested in chipseq are comparing it to the libraries listed below
Sorting:
- ATAC-seq peak-calling and QC analysis pipeline☆220Nov 20, 2025Updated 3 months ago
- Analysis of Chromosome Conformation Capture data (Hi-C)☆108Nov 20, 2025Updated 3 months ago
- ChIP-seq analysis notes from Ming Tang☆842Aug 5, 2024Updated last year
- RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.☆1,212Updated this week
- RNA-seq analysis pipeline for detection of gene-fusions☆171Feb 10, 2026Updated 2 weeks ago
- MACS -- Model-based Analysis of ChIP-Seq☆767Updated this week
- ENCODE ChIP-seq pipeline☆277Feb 15, 2024Updated 2 years ago
- Nascent Transcription Processing Pipeline☆22Nov 20, 2025Updated 3 months ago
- Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair☆187Feb 12, 2026Updated 2 weeks ago
- Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-dropl…☆313Updated this week
- Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream …☆107Feb 17, 2026Updated last week
- Please consider using/contributing to https://github.com/nf-core/sarek☆18Jan 3, 2019Updated 7 years ago
- Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing☆550Updated this week
- Tools to process and analyze deep sequencing data.☆752Jul 23, 2025Updated 7 months ago
- Application for making ENCODE Blacklists☆334Apr 23, 2021Updated 4 years ago
- UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies☆27May 13, 2025Updated 9 months ago
- Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq☆89Updated this week
- ChIP peak Annotation, Comparison and Visualization☆250Nov 4, 2025Updated 3 months ago
- MNase-seq analysis pipeline using BWA and DANPOS2.☆13Updated this week
- Intro to ChIPseq using HPC☆319Jan 30, 2023Updated 3 years ago
- Pipeline to fetch metadata and raw FastQ files from public databases☆187Feb 8, 2026Updated 2 weeks ago
- ENCODE Uniform processing pipeline for ChIP-seq☆124Mar 23, 2020Updated 5 years ago
- Nanopore demultiplexing, QC and alignment pipeline☆219Nov 20, 2025Updated 3 months ago
- This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to…☆62Jul 20, 2020Updated 5 years ago
- A small-RNA sequencing analysis pipeline☆99Jan 7, 2026Updated last month
- circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data☆58Jan 31, 2026Updated last month
- Transcript assembly and quantification for RNA-Seq☆489Dec 26, 2025Updated 2 months ago
- Chromatin States Map in mouse embryonic stem cell☆19Apr 11, 2018Updated 7 years ago
- ENCODE ATAC-seq pipeline☆446Jul 18, 2024Updated last year
- A modular Hi-C mapping pipeline☆101Dec 5, 2024Updated last year
- ☆19Jun 8, 2023Updated 2 years ago
- k-mer similarity analysis pipeline☆21Nov 20, 2025Updated 3 months ago
- ☆17Apr 27, 2023Updated 2 years ago
- Nextflow pipeline that runs DESeq2 on data processed with the nextflow RNAseq pipeline☆13Dec 2, 2025Updated 2 months ago
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆431Mar 28, 2024Updated last year
- Bead-based single-cell atac processing☆33Nov 13, 2021Updated 4 years ago
- ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).☆26Feb 3, 2022Updated 4 years ago
- Detecting sites of genomic enrichment☆199May 8, 2023Updated 2 years ago
- Demultiplexing pipeline for sequencing data☆52Feb 12, 2026Updated 2 weeks ago