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https://github.com/databio/awesome-atac-analysis

Links to ATAC-seq analysis tools
https://github.com/databio/awesome-atac-analysis

List: awesome-atac-analysis

Last synced: about 1 month ago
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Links to ATAC-seq analysis tools

Host: GitHub
URL: https://github.com/databio/awesome-atac-analysis
Owner: databio
Created: 2020-01-28T16:30:43.000Z (almost 5 years ago)
Default Branch: master
Last Pushed: 2021-08-24T18:42:29.000Z (over 3 years ago)
Last Synced: 2024-11-09T02:02:30.651Z (about 1 month ago)
Homepage:
Size: 84 KB
Stars: 50
Watchers: 20
Forks: 6
Open Issues: 0
Metadata Files:
- Readme: README.md

Awesome Lists containing this project

ultimate-awesome - awesome-atac-analysis - Links to ATAC-seq analysis tools. (Other Lists / Monkey C Lists)

README

        # Awesome ATAC-seq analysis

A collection of tools for analysis of chromatin accessibility data.

## QC

- [ATACseqQC](https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html)

- [ATAqC](https://github.com/kundajelab/ataqc)

- [ataqv](https://github.com/ParkerLab/ataqv)

## Single-cell

- [Accessibility Pattern based Epigenomic Clustering (APEC)](https://github.com/QuKunLab/APEC)

- [AMULET](https://github.com/UcarLab/AMULET): A count based method for detecting multiplets from single nucleus ATAC-seq (snATAC-seq) data

- [ArchR: Analysis of Regulatory Chromatin in R](https://github.com/GreenleafLab/ArchR)

- [Bead-based scATAC-seq data Processing (BAP)](https://github.com/caleblareau/bap)

- [Brockman Representation Of Chromatin by K-mers in Mark-Associated Nucleotides.](https://carldeboer.github.io/brockman.html)

- [Cell Ranger ATAC](https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac)

- [chromVAR](https://github.com/GreenleafLab/chromVAR)

- [Cicero](https://cole-trapnell-lab.github.io/cicero-release/)

- [cisTopic](https://github.com/aertslab/cisTopic)

- [destin](https://github.com/urrutiag/destin)

- [epiScanpy](https://github.com/colomemaria/epiScanpy)

- [scABC - single cell Accessibility Based Clustering](https://github.com/SUwonglab/scABC)

- [scAI - single cell Aggregation and Integration method for analyzing single cell multi-omics data](https://github.com/amsszlh/scAI)

- [SCALE](https://github.com/jsxlei/SCALE)

- [SCATE](https://github.com/zji90/SCATE)

- [Scasat (single-cell ATAC-seq analysis tool)](https://github.com/ManchesterBioinference/Scasat)

- [scATAC-pro](https://www.biorxiv.org/content/10.1101/824326v1.abstract)

- [sc-compReg](https://github.com/SUwonglab/sc-compReg)

- [scOpen](https://www.biorxiv.org/content/10.1101/865931v1.abstract)

- [SCRAT](https://zhiji.shinyapps.io/scrat/)

- [signac](https://satijalab.org/signac/)

- [SnapATAC (Single Nucleus Analysis Pipeline for ATAC-seq)](https://github.com/r3fang/SnapATAC)

- [TimeReg](https://github.com/SUwonglab/TimeReg)

## Raw data processing pipelines

- [AIAP: a Quality Control and Integrative Analysis Package](https://github.com/Zhang-lab/ATAC-seq_QC_analysis)

- [ATAC-pipe](https://academic.oup.com/bib/article/20/5/1934/5047123)

- [ATAC2GRN](https://github.com/ChioriniLab/ATAC2GRN)

- [ATACProc: a pipeline for processing ATAC-seq data](https://github.com/ay-lab/ATACProc)

- [Basepair](https://www.basepairtech.com/analysis/atac-seq/) 

- [A bioinformatic analysis pipeline for bulk ATAC-seq](https://github.com/shengyongniu/bulk_ATAC_seq)

- [CIPHER](https://github.com/c-guzman/cipher-workflow-platform)

- [ENCODE ATAC-seq pipeline](https://github.com/ENCODE-DCC/atac-seq-pipeline)

- [esATAC](https://www.bioconductor.org/packages/release/bioc/html/esATAC.html)

- [GUAVA: A Graphical User Interface for the Analysis and Visualization of ATAC-seq Data](https://github.com/MayurDivate/GUAVA)

- [I-ATAC](https://www.jax.org/research-and-faculty/resources/i-atac#) - interactive pipeline for the management and pre-processing of ATAC-seq samples.

- [nfcore/atacseq](https://github.com/nf-core/atacseq)

- [PEPATAC](http://pepatac.databio.org/en/latest/)

- [pyflow-atacseq](https://github.com/crazyhottommy/pyflow-ATACseq)

- [seq2science](https://github.com/vanheeringen-lab/seq2science)

- [snakePipes ATAC-seq](https://snakepipes.readthedocs.io/en/latest/content/workflows/ATAC-seq.html)

## Peak callers

- [F-Seq](http://fureylab.web.unc.edu/software/fseq/)

- [Genrich](https://github.com/jsh58/Genrich)

- [HMMRATAC](https://github.com/LiuLabUB/HMMRATAC)

- [HOMER](http://homer.ucsd.edu/homer/)

- [Hotspot2](https://github.com/Altius/hotspot2)

- [MACS](https://github.com/taoliu/MACS)

- [PeaKDEck](https://www.ccmp.ox.ac.uk/peakdeck)

## Motif enrichment/TF footprinting/TFBS

- [BiFET](https://github.com/UcarLab/BiFET)

- [BinDNase](https://research.cs.aalto.fi/csb/software/index.shtml)

- [CENTIPEDE](http://centipede.uchicago.edu/)

- [DNase2TF](https://sourceforge.net/projects/dnase2tfr/)

- [enrichTF](https://www.bioconductor.org/packages/release/bioc/html/enrichTF.html)

- [HINT-ATAC](https://link.springer.com/article/10.1186/s13059-019-1642-2)

- [HOMER](http://homer.ucsd.edu/homer/)

- [MEDEA](https://github.com/BulykLab/MEDEA)

- [MEME Suite](http://meme-suite.org/)

- [MMARGE](https://github.com/vlink/marge/)

- [PIQ](http://piq.csail.mit.edu/)

- [Romulus](https://github.com/ajank/Romulus)

- [TEPIC](https://github.com/schulzlab/TEPIC)

- [TOBIAS](https://github.com/loosolab/TOBIAS)

- [TRACE](https://www.biorxiv.org/content/10.1101/801001v1.abstract)

- [Wellington](https://github.com/jpiper/pyDNase)

## Differential accessibility

- [ALTRE](https://mathelab.github.io/ALTRE/)

- [DAStk](https://github.com/Dowell-Lab/DAStk)

- [diffTF](https://difftf.readthedocs.io/en/latest/)

## Nucleosome positioning

- [HMMRATAC](https://academic.oup.com/nar/article/47/16/e91/5519166)

- [NucleoATAC](https://nucleoatac.readthedocs.io/en/latest/)

- [NucTools](https://link.springer.com/article/10.1186/s12864-017-3580-2)

## Region enrichment

- [Annotatr](https://bioconductor.org/packages/release/bioc/html/annotatr.html)

- [COCOA](http://code.databio.org/COCOA/index.html)

- [GIGGLE](https://github.com/ryanlayer/giggle)

- [GREAT](http://great.stanford.edu/public/html/)

- [LOLA](https://github.com/nsheff/LOLA)

- [regioneR](http://bioconductor.org/packages/release/bioc/html/regioneR.html)

## Uncategorized

- [ATACgraph](https://github.com/RitataLU/ATACgraph): post alignment QC and differential analyses modules

- [AtacWorks](https://github.com/clara-genomics/AtacWorks): correct noisy/low-quality ATAC-seq data to obtain improved peak calls

- [BeCorrect](https://github.com/Zhang-lab/BeCorrect): correct the batch effect of ATAC-seq signal density for visualization purposes

- [CoRE-ATAC](https://github.com/UcarLab/CoRE-ATAC/): Classification of Regulatory Elements with ATAC-seq (predict Promoters, Enhancers, and Inuslators)

- [PEAS](https://github.com/UcarLab/PEAS): Predict Enhancers from ATAC-seq

- [PECA](https://github.com/SUwonglab/PECA): infer context specific gene regulatory network from paired gene expression and chromatin accessibility data

- [seqOutBias](https://guertinlab.github.io/seqOutBias/): correction of enzymatic sequence bias

- [sequence bias correction](https://github.com/txje/sequence-bias-adjustment)