https://github.com/databio/awesome-atac-analysis
Links to ATAC-seq analysis tools
Science Score: 23.0%
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 5 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org, springer.com -
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○Scientific vocabulary similarity
Low similarity (6.4%) to scientific vocabulary
Last synced: 10 months ago
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Repository
Links to ATAC-seq analysis tools
Statistics
- Stars: 69
- Watchers: 19
- Forks: 6
- Open Issues: 0
- Releases: 0
Created over 6 years ago
· Last pushed almost 5 years ago
Metadata Files
Readme
README.md
Awesome ATAC-seq analysis
A collection of tools for analysis of chromatin accessibility data.
QC
Single-cell
- Accessibility Pattern based Epigenomic Clustering (APEC)
- AMULET: A count based method for detecting multiplets from single nucleus ATAC-seq (snATAC-seq) data
- ArchR: Analysis of Regulatory Chromatin in R
- Bead-based scATAC-seq data Processing (BAP)
- Brockman Representation Of Chromatin by K-mers in Mark-Associated Nucleotides.
- Cell Ranger ATAC
- chromVAR
- Cicero
- cisTopic
- destin
- epiScanpy
- scABC - single cell Accessibility Based Clustering
- scAI - single cell Aggregation and Integration method for analyzing single cell multi-omics data
- SCALE
- SCATE
- Scasat (single-cell ATAC-seq analysis tool)
- scATAC-pro
- sc-compReg
- scOpen
- SCRAT
- signac
- SnapATAC (Single Nucleus Analysis Pipeline for ATAC-seq)
- TimeReg
Raw data processing pipelines
- AIAP: a Quality Control and Integrative Analysis Package
- ATAC-pipe
- ATAC2GRN
- ATACProc: a pipeline for processing ATAC-seq data
- Basepair
- A bioinformatic analysis pipeline for bulk ATAC-seq
- CIPHER
- ENCODE ATAC-seq pipeline
- esATAC
- GUAVA: A Graphical User Interface for the Analysis and Visualization of ATAC-seq Data
- I-ATAC - interactive pipeline for the management and pre-processing of ATAC-seq samples.
- nfcore/atacseq
- PEPATAC
- pyflow-atacseq
- seq2science
- snakePipes ATAC-seq
Peak callers
Motif enrichment/TF footprinting/TFBS
- BiFET
- BinDNase
- CENTIPEDE
- DNase2TF
- enrichTF
- HINT-ATAC
- HOMER
- MEDEA
- MEME Suite
- MMARGE
- PIQ
- Romulus
- TEPIC
- TOBIAS
- TRACE
- Wellington
Differential accessibility
Nucleosome positioning
Region enrichment
Uncategorized
- ATACgraph: post alignment QC and differential analyses modules
- AtacWorks: correct noisy/low-quality ATAC-seq data to obtain improved peak calls
- BeCorrect: correct the batch effect of ATAC-seq signal density for visualization purposes
- CoRE-ATAC: Classification of Regulatory Elements with ATAC-seq (predict Promoters, Enhancers, and Inuslators)
- PEAS: Predict Enhancers from ATAC-seq
- PECA: infer context specific gene regulatory network from paired gene expression and chromatin accessibility data
- seqOutBias: correction of enzymatic sequence bias
- sequence bias correction
Owner
- Name: Databio
- Login: databio
- Kind: organization
- Location: University of Virginia
- Website: https://databio.org
- Repositories: 88
- Profile: https://github.com/databio
Solving problems in computational biology
GitHub Events
Total
- Watch event: 18
- Fork event: 1
Last Year
- Watch event: 18
- Fork event: 1
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Last synced: over 1 year ago
All Time
- Total issues: 0
- Total pull requests: 2
- Average time to close issues: N/A
- Average time to close pull requests: 32 minutes
- Total issue authors: 0
- Total pull request authors: 2
- Average comments per issue: 0
- Average comments per pull request: 1.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
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- jdidion (1)
- spekulatius (1)