ATACCoGAPS

DOI: 10.18129/B9.bioc.ATACCoGAPS    

This is the development version of ATACCoGAPS; to use it, please install the devel version of Bioconductor.

Analysis Tools for scATACseq Data with CoGAPS

Bioconductor version: Development (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>

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

Installation

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

 

HTML R Script ATACCoGAPS
PDF   Reference Manual
Text   NEWS

Details

biocViews Bayesian, Clustering, DimensionReduction, Epigenetics, ResearchField, SingleCell, Software, Transcription
Version 0.99.13
In Bioconductor since BioC 3.16 (R-4.2)
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_0.99.13.tar.gz
Windows Binary ATACCoGAPS_0.99.13.zip
macOS Binary (x86_64)
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
Package Short Url https://bioconductor.org/packages/ATACCoGAPS/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: