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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 (3.18)

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>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
ATACCoGAPS HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, Clustering, DimensionReduction, Epigenetics, ResearchField, SingleCell, Software, Transcription
Version 1.3.0
In Bioconductor since BioC 3.16 (R-4.2) (1 year)
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
Linking To
Suggests knitr, viridis
System Requirements
Enhances
URL
Bug Reports https://github.com/FertigLab/ATACCoGAPS/issues
See More
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_1.3.0.tar.gz
Windows Binary
macOS Binary (x86_64) ATACCoGAPS_1.3.0.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