{"id":14110359,"url":"https://github.com/databio/awesome-atac-analysis","last_synced_at":"2026-02-13T06:17:27.503Z","repository":{"id":53337314,"uuid":"236781912","full_name":"databio/awesome-atac-analysis","owner":"databio","description":"Links to ATAC-seq analysis tools","archived":false,"fork":false,"pushed_at":"2021-08-24T18:42:29.000Z","size":86,"stargazers_count":69,"open_issues_count":0,"forks_count":6,"subscribers_count":19,"default_branch":"master","last_synced_at":"2025-09-06T08:02:17.921Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/databio.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-01-28T16:30:43.000Z","updated_at":"2025-08-06T12:06:52.000Z","dependencies_parsed_at":"2022-09-11T03:21:38.749Z","dependency_job_id":null,"html_url":"https://github.com/databio/awesome-atac-analysis","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/databio/awesome-atac-analysis","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fawesome-atac-analysis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fawesome-atac-analysis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fawesome-atac-analysis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fawesome-atac-analysis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/databio","download_url":"https://codeload.github.com/databio/awesome-atac-analysis/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fawesome-atac-analysis/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274776752,"owners_count":25347639,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-09-12T02:00:09.324Z","response_time":60,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-08-14T10:02:48.885Z","updated_at":"2026-02-13T06:17:22.452Z","avatar_url":"https://github.com/databio.png","language":null,"funding_links":[],"categories":["Other Lists"],"sub_categories":["TeX Lists"],"readme":"# Awesome ATAC-seq analysis\n\nA collection of tools for analysis of chromatin accessibility data.\n\n## QC\n\n- [ATACseqQC](https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html)\n- [ATAqC](https://github.com/kundajelab/ataqc)\n- [ataqv](https://github.com/ParkerLab/ataqv)\n\n## Single-cell\n\n- [Accessibility Pattern based Epigenomic Clustering (APEC)](https://github.com/QuKunLab/APEC)\n- [AMULET](https://github.com/UcarLab/AMULET): A count based method for detecting multiplets from single nucleus ATAC-seq (snATAC-seq) data\n- [ArchR: Analysis of Regulatory Chromatin in R](https://github.com/GreenleafLab/ArchR)\n- [Bead-based scATAC-seq data Processing (BAP)](https://github.com/caleblareau/bap)\n- [Brockman Representation Of Chromatin by K-mers in Mark-Associated Nucleotides.](https://carldeboer.github.io/brockman.html)\n- [Cell Ranger ATAC](https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac)\n- [chromVAR](https://github.com/GreenleafLab/chromVAR)\n- [Cicero](https://cole-trapnell-lab.github.io/cicero-release/)\n- [cisTopic](https://github.com/aertslab/cisTopic)\n- [destin](https://github.com/urrutiag/destin)\n- [epiScanpy](https://github.com/colomemaria/epiScanpy)\n- [scABC - single cell Accessibility Based Clustering](https://github.com/SUwonglab/scABC)\n- [scAI - single cell Aggregation and Integration method for analyzing single cell multi-omics data](https://github.com/amsszlh/scAI)\n- [SCALE](https://github.com/jsxlei/SCALE)\n- [SCATE](https://github.com/zji90/SCATE)\n- [Scasat (single-cell ATAC-seq analysis tool)](https://github.com/ManchesterBioinference/Scasat)\n- [scATAC-pro](https://www.biorxiv.org/content/10.1101/824326v1.abstract)\n- [sc-compReg](https://github.com/SUwonglab/sc-compReg)\n- [scOpen](https://www.biorxiv.org/content/10.1101/865931v1.abstract)\n- [SCRAT](https://zhiji.shinyapps.io/scrat/)\n- [signac](https://satijalab.org/signac/)\n- [SnapATAC (Single Nucleus Analysis Pipeline for ATAC-seq)](https://github.com/r3fang/SnapATAC)\n- [TimeReg](https://github.com/SUwonglab/TimeReg)\n\n## Raw data processing pipelines\n\n- [AIAP: a Quality Control and Integrative Analysis Package](https://github.com/Zhang-lab/ATAC-seq_QC_analysis)\n- [ATAC-pipe](https://academic.oup.com/bib/article/20/5/1934/5047123)\n- [ATAC2GRN](https://github.com/ChioriniLab/ATAC2GRN)\n- [ATACProc: a pipeline for processing ATAC-seq data](https://github.com/ay-lab/ATACProc)\n- [Basepair](https://www.basepairtech.com/analysis/atac-seq/) \n- [A bioinformatic analysis pipeline for bulk ATAC-seq](https://github.com/shengyongniu/bulk_ATAC_seq)\n- [CIPHER](https://github.com/c-guzman/cipher-workflow-platform)\n- [ENCODE ATAC-seq pipeline](https://github.com/ENCODE-DCC/atac-seq-pipeline)\n- [esATAC](https://www.bioconductor.org/packages/release/bioc/html/esATAC.html)\n- [GUAVA: A Graphical User Interface for the Analysis and Visualization of ATAC-seq Data](https://github.com/MayurDivate/GUAVA)\n- [I-ATAC](https://www.jax.org/research-and-faculty/resources/i-atac#) - interactive pipeline for the management and pre-processing of ATAC-seq samples.\n- [nfcore/atacseq](https://github.com/nf-core/atacseq)\n- [PEPATAC](http://pepatac.databio.org/en/latest/)\n- [pyflow-atacseq](https://github.com/crazyhottommy/pyflow-ATACseq)\n- [seq2science](https://github.com/vanheeringen-lab/seq2science)\n- [snakePipes ATAC-seq](https://snakepipes.readthedocs.io/en/latest/content/workflows/ATAC-seq.html)\n\n## Peak callers\n\n- [F-Seq](http://fureylab.web.unc.edu/software/fseq/)\n- [Genrich](https://github.com/jsh58/Genrich)\n- [HMMRATAC](https://github.com/LiuLabUB/HMMRATAC)\n- [HOMER](http://homer.ucsd.edu/homer/)\n- [Hotspot2](https://github.com/Altius/hotspot2)\n- [MACS](https://github.com/taoliu/MACS)\n- [PeaKDEck](https://www.ccmp.ox.ac.uk/peakdeck)\n\n## Motif enrichment/TF footprinting/TFBS\n\n- [BiFET](https://github.com/UcarLab/BiFET)\n- [BinDNase](https://research.cs.aalto.fi/csb/software/index.shtml)\n- [CENTIPEDE](http://centipede.uchicago.edu/)\n- [DNase2TF](https://sourceforge.net/projects/dnase2tfr/)\n- [enrichTF](https://www.bioconductor.org/packages/release/bioc/html/enrichTF.html)\n- [HINT-ATAC](https://link.springer.com/article/10.1186/s13059-019-1642-2)\n- [HOMER](http://homer.ucsd.edu/homer/)\n- [MEDEA](https://github.com/BulykLab/MEDEA)\n- [MEME Suite](http://meme-suite.org/)\n- [MMARGE](https://github.com/vlink/marge/)\n- [PIQ](http://piq.csail.mit.edu/)\n- [Romulus](https://github.com/ajank/Romulus)\n- [TEPIC](https://github.com/schulzlab/TEPIC)\n- [TOBIAS](https://github.com/loosolab/TOBIAS)\n- [TRACE](https://www.biorxiv.org/content/10.1101/801001v1.abstract)\n- [Wellington](https://github.com/jpiper/pyDNase)\n\n## Differential accessibility\n\n- [ALTRE](https://mathelab.github.io/ALTRE/)\n- [DAStk](https://github.com/Dowell-Lab/DAStk)\n- [diffTF](https://difftf.readthedocs.io/en/latest/)\n\n## Nucleosome positioning\n\n- [HMMRATAC](https://academic.oup.com/nar/article/47/16/e91/5519166)\n- [NucleoATAC](https://nucleoatac.readthedocs.io/en/latest/)\n- [NucTools](https://link.springer.com/article/10.1186/s12864-017-3580-2)\n\n## Region enrichment\n\n- [Annotatr](https://bioconductor.org/packages/release/bioc/html/annotatr.html)\n- [COCOA](http://code.databio.org/COCOA/index.html)\n- [GIGGLE](https://github.com/ryanlayer/giggle)\n- [GREAT](http://great.stanford.edu/public/html/)\n- [LOLA](https://github.com/nsheff/LOLA)\n- [regioneR](http://bioconductor.org/packages/release/bioc/html/regioneR.html)\n\n## Uncategorized\n\n- [ATACgraph](https://github.com/RitataLU/ATACgraph): post alignment QC and differential analyses modules\n- [AtacWorks](https://github.com/clara-genomics/AtacWorks): correct noisy/low-quality ATAC-seq data to obtain improved peak calls\n- [BeCorrect](https://github.com/Zhang-lab/BeCorrect): correct the batch effect of ATAC-seq signal density for visualization purposes\n- [CoRE-ATAC](https://github.com/UcarLab/CoRE-ATAC/): Classification of Regulatory Elements with ATAC-seq (predict Promoters, Enhancers, and Inuslators)\n- [PEAS](https://github.com/UcarLab/PEAS): Predict Enhancers from ATAC-seq\n- [PECA](https://github.com/SUwonglab/PECA): infer context specific gene regulatory network from paired gene expression and chromatin accessibility data\n- [seqOutBias](https://guertinlab.github.io/seqOutBias/): correction of enzymatic sequence bias\n- [sequence bias correction](https://github.com/txje/sequence-bias-adjustment)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fawesome-atac-analysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatabio%2Fawesome-atac-analysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fawesome-atac-analysis/lists"}