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awesome-atac-analysis
Links to ATAC-seq analysis tools
https://github.com/databio/awesome-atac-analysis
- ATACseqQC
- ATAqC
- ataqv
- 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)
- 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
- 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
- F-Seq
- Genrich
- HMMRATAC
- HOMER
- Hotspot2
- MACS
- PeaKDEck
- BiFET
- BinDNase
- CENTIPEDE
- DNase2TF
- enrichTF
- HINT-ATAC
- HOMER
- MEDEA
- MEME Suite
- MMARGE
- PIQ
- Romulus
- TEPIC
- TOBIAS
- TRACE
- Wellington
- ALTRE
- DAStk
- diffTF
- HMMRATAC
- NucleoATAC
- NucTools
- Annotatr
- COCOA
- GIGGLE
- GREAT
- LOLA
- regioneR
- ATACgraph
- AtacWorks - quality ATAC-seq data to obtain improved peak calls
- BeCorrect - seq signal density for visualization purposes
- CoRE-ATAC - seq (predict Promoters, Enhancers, and Inuslators)
- PEAS - seq
- PECA
- seqOutBias
- sequence bias correction
Programming Languages
Keywords
atac-seq
13
dnase-seq
4
chromatin-accessibiity
3
bioinformatics
3
single-cell
3
snakemake
2
pipeline
2
epigenetics
2
sequencing
2
rna-seq
2
bioinformatics-pipeline
2
footprinting
2
peak-caller
2
r
2
single-cell-atac-seq
2
chip-seq
2
single-cell-analysis
1
machine-learning-algorithms
1
scrna-seq
1
scatac-seq
1
comparative-regulatory-analysis
1
pipelines
1
quality-control
1
software
1
tool
1
visualization
1
scatac
1
genomics
1
epigenomics
1
workflows
1
sra
1
reproducible-research
1
ngs
1
fastq
1
workflow
1
nf-core
1
nextflow
1
gene-regulatory-network
1
gene-expression
1
transcription-factor-binding
1
statistical-tests
1
bioconductor
1
python
1
poisson-equation
1
macs
1
peak-detection
1
machine-learning
1
bulk-atac-seq
1
qc
1
macs2
1