ATACCoGAPS

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.20 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see ATACCoGAPS.

Analysis Tools for scATACseq Data with CoGAPS

Bioconductor version: Release (3.20)

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 "4.4") 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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bayesian, Clustering, DimensionReduction, Epigenetics, ResearchField, SingleCell, Software, Transcription
Version	1.8.0
In Bioconductor since	BioC 3.16 (R-4.2) (2 years)
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
System Requirements
URL
Bug Reports	https://github.com/FertigLab/ATACCoGAPS/issues

Suggests	knitr, viridis
Linking To
Enhances
Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
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