ATACCoGAPS

DOI: 10.18129/B9.bioc.ATACCoGAPS  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see ATACCoGAPS.

Analysis Tools for scATACseq Data with CoGAPS

Bioconductor version: 3.16

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 jhmi.edu>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ATACCoGAPS")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ATACCoGAPS")

 

HTML	R Script	ATACCoGAPS
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, Clustering, DimensionReduction, Epigenetics, ResearchField, SingleCell, Software, Transcription
Version	1.0.0
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
LinkingTo
Suggests	knitr, viridis
SystemRequirements
Enhances
URL
BugReports	https://github.com/FertigLab/ATACCoGAPS/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ATACCoGAPS_1.0.0.tar.gz
Windows Binary	ATACCoGAPS_1.0.0.zip
macOS Binary (x86_64)	ATACCoGAPS_1.0.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/ATACCoGAPS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ATACCoGAPS
Bioc Package Browser	https://code.bioconductor.org/browse/ATACCoGAPS/
Package Short Url	https://bioconductor.org/packages/ATACCoGAPS/
Package Downloads Report	Download Stats