DESCRIPTION

Package: ATACCoGAPS
Title: Analysis Tools for scATACseq Data with CoGAPS
Version: 0.99.13
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