Package: ATACCoGAPS
Title: Analysis Tools for scATACseq Data with CoGAPS
Version: 1.0.0
Authors@R: 
    person(given = "Rossin",
           family = "Erbe",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-3423-2104"),
           email = "rerbe1@jhmi.edu")
Description: 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.
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
biocViews: Software, ResearchField, Epigenetics, SingleCell,
        Transcription, Bayesian, Clustering, DimensionReduction
BiocType: Software
RoxygenNote: 7.2.0
Encoding: UTF-8
Suggests: knitr, viridis
BugReports: https://github.com/FertigLab/ATACCoGAPS/issues
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/ATACCoGAPS
git_branch: RELEASE_3_16
git_last_commit: f320695
git_last_commit_date: 2022-11-01
Date/Publication: 2023-02-28
NeedsCompilation: no
Packaged: 2023-02-28 20:57:36 UTC; biocbuild
Author: Rossin Erbe [aut, cre] (<https://orcid.org/0000-0002-3423-2104>)
Maintainer: Rossin Erbe <rerbe1@jhmi.edu>
Built: R 4.2.2; ; 2023-03-01 05:34:01 UTC; unix
