awesome-atac-analysis
Links to ATAC-seq analysis tools
https://github.com/databio/awesome-atac-analysis
Last synced: about 2 hours ago
JSON representation
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QC
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Single-cell
- scOpen
- Brockman Representation Of Chromatin by K-mers in Mark-Associated Nucleotides.
- Cell Ranger ATAC
- epiScanpy
- scATAC-pro
- SCRAT
- signac
- Accessibility Pattern based Epigenomic Clustering (APEC)
- AMULET - seq (snATAC-seq) data
- ArchR: Analysis of Regulatory Chromatin in R
- Bead-based scATAC-seq data Processing (BAP)
- chromVAR
- Cicero
- cisTopic
- destin
- 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)
- sc-compReg
- SnapATAC (Single Nucleus Analysis Pipeline for ATAC-seq)
- TimeReg
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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
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Peak callers
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Motif enrichment/TF footprinting/TFBS
- BinDNase
- CENTIPEDE
- DNase2TF
- enrichTF
- HINT-ATAC
- MEME Suite
- PIQ
- TRACE
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- HINT-ATAC
- 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
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Differential accessibility
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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
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Region enrichment
Programming Languages
Categories
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