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awesome-atac-analysis

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

Last synced: 6 days ago
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QC
- ATACseqQC
- ATAqC
- ataqv
Single-cell
Raw data processing pipelines
- ATAC-pipe
- Basepair
- esATAC
- I-ATAC - interactive pipeline for the management and pre-processing of ATAC-seq samples.
- snakePipes ATAC-seq
- PEPATAC
- AIAP: a Quality Control and Integrative Analysis Package
- ATAC2GRN
- ATACProc: a pipeline for processing ATAC-seq data
- A bioinformatic analysis pipeline for bulk ATAC-seq
- CIPHER
- ENCODE ATAC-seq pipeline
- GUAVA: A Graphical User Interface for the Analysis and Visualization of ATAC-seq Data
- nfcore/atacseq
- pyflow-atacseq
- seq2science
Peak callers
- PeaKDEck
- F-Seq
- Genrich
- HMMRATAC
- Hotspot2
- MACS
- HOMER
Motif enrichment/TF footprinting/TFBS
- BinDNase
- CENTIPEDE
- DNase2TF
- enrichTF
- HINT-ATAC
- MEME Suite
- PIQ
- TRACE
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- MEME Suite
- HINT-ATAC
- BiFET
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
Differential accessibility
- diffTF
Nucleosome positioning
- HMMRATAC
- NucleoATAC
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
- NucTools
Region enrichment
- Annotatr
- COCOA
- GREAT
- regioneR

Programming Languages

Python 9 R 7 Shell 4 HTML 3 C++ 3 MATLAB 2 Java 1 C 1 Nextflow 1 Jupyter Notebook 1

Categories

Motif enrichment/TF footprinting/TFBS 53 Nucleosome positioning 42 Single-cell 23 Raw data processing pipelines 16 Peak callers 7 Region enrichment 4 QC 3 Differential accessibility 1

Sub Categories

Keywords

atac-seq 10 single-cell 3 sequencing 2 bioinformatics-pipeline 2 chromatin-accessibiity 2 pipeline 2 single-cell-atac-seq 2 snakemake 2 r 2 dnase-seq 2 bioinformatics 2 epigenetics 2 scatac 1 genomics 1 epigenomics 1 bead-doublets 1 visualization 1 pipelines 1 comparative-regulatory-analysis 1 tool 1 scatac-seq 1 scrna-seq 1 software 1 machine-learning-algorithms 1 quality-control 1 transcription-factor-binding 1 statistical-tests 1 footprinting 1 bioconductor 1 peak-detection 1 peak-caller 1 machine-learning 1 workflows 1 sra 1 rna-seq 1 reproducible-research 1 ngs 1 fastq 1 chip-seq 1 workflow 1 nf-core 1 nextflow 1 bulk-atac-seq 1 qc 1 macs2 1 atacseqqc 1 single-cell-analysis 1