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("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 |
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 |
See More
| Suggests | knitr, viridis |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| 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 [email protected]:packages/ATACCoGAPS |
| Package Short Url | https://bioconductor.org/packages/ATACCoGAPS/ |
| Package Downloads Report | Download Stats |