A collection of tools for analysis of chromatin accessibility data.
- 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
- 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
- BiFET
- BinDNase
- CENTIPEDE
- DNase2TF
- enrichTF
- HINT-ATAC
- HOMER
- MEDEA
- MEME Suite
- MMARGE
- PIQ
- Romulus
- TEPIC
- TOBIAS
- TRACE
- Wellington
- 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