DOI: 10.18129/B9.bioc.ATACCoGAPS    

This is the development version of ATACCoGAPS; for the stable release version, see ATACCoGAPS.

Analysis Tools for scATACseq Data with CoGAPS

Bioconductor version: Development (3.17)

Provides tools for running the CoGAPS algorithm (Fertig et al, 2010) on single-cell ATAC sequencing data and analysis of the results. Can be used to perform analyses at the level of genes, motifs, TFs, or pathways. Additionally provides tools for transfer learning and data integration with single-cell RNA sequencing data.

Author: Rossin Erbe [aut, cre]

Maintainer: Rossin Erbe <rerbe1 at>

Citation (from within R, enter citation("ATACCoGAPS")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


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biocViews Bayesian, Clustering, DimensionReduction, Epigenetics, ResearchField, SingleCell, Software, Transcription
Version 1.1.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
License Artistic-2.0
Depends R (>= 4.2.0), CoGAPS(>= 3.5.13)
Imports gtools, GenomicRanges, projectR, TFBSTools, GeneOverlap, msigdbr, tidyverse, gplots, motifmatchr, chromVAR, GenomicFeatures, IRanges, fgsea, rGREAT, JASPAR2016, Homo.sapiens, Mus.musculus, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, stringr, dplyr
Suggests knitr, viridis
Depends On Me
Imports Me
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