Package: MOCHA
Type: Package
Title: Modeling for Single-Cell Open Chromatin Analysis
Version: 0.1.0
Authors@R: 
    c(person(given = "Samir",
           family = "Rachid Zaim",
           role = c("aut", "ctb"),
           email = "samir.rachidzaim@alleninstitute.org"),
    person(given = "Mark-Phillip",
           family = "Pebworth",
           role = c("aut", "ctb"),
           email = "markphillip.pebworth@alleninstitute.org"),
    person(given = "Imran",
           family = "McGrath",
           role = c("aut", "cre"),
           email = "imran.mcgrath@alleninstitute.org"),
    person(given = "Lauren",
           family = "Okada",
           role = c("aut", "ctb"),
           email = "lauren.okada@alleninstitute.org"),
    person(given = "Xiaojun",
           family = "Li",
           role = c("aut", "ctb"),
           email = "xiaojun.li@alleninstitute.org")
    )
Maintainer: Imran McGrath <imran.mcgrath@alleninstitute.org>
Description: A statistical framework and analysis tool for open chromatin 
  analysis designed specifically for single cell ATAC-seq (Assay for 
  Transposase-Accessible Chromatin) data, after cell type/cluster 
  identification. These novel modules remove unwanted technical variation, 
  identify open chromatin, robustly models repeated measures in single cell 
  data, implement advanced statistical frameworks to model zero-inflation for 
  differential and co-accessibility analyses, and integrate with existing 
  databases and modules for downstream analyses to reveal biological insights. 
  MOCHA provides a statistical foundation for complex downstream analysis to 
  help advance the potential of single cell ATAC-seq for applied studies. 
  Methods for zero-inflated statistics are as described in: 
  Ghazanfar, S., Lin, Y., Su, X. et al. (2020) <doi:10.1038/s41592-020-0885-x>.
  Pimentel, Ronald Silva, "Kendall's Tau and Spearman's Rho for Zero-Inflated 
  Data" (2009) <https://scholarworks.wmich.edu/dissertations/721/>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.1
Depends: R (>= 3.5.0)
Imports: data.table, plyranges, dplyr, GenomicRanges, RaggedExperiment,
        MultiAssayExperiment, SummarizedExperiment, stringr, ggbio,
        wCorr, magrittr, rlang, AnnotationDbi, BiocGenerics,
        GenomeInfoDb, GenomicFeatures, IRanges, OrganismDbi, S4Vectors,
        assertthat, biovizBase, ensembldb, ggplot2, ggrepel,
        matrixStats, methods, qvalue, scales, tidyr, ggridges
Suggests: ArchR, RMariaDB, motifmatchr, BiocManager,
        TxDb.Hsapiens.UCSC.hg38.refGene, org.Hs.eg.db,
        BSgenome.Hsapiens.UCSC.hg19, withr, knitr, rmarkdown, testthat
        (>= 3.0.0)
Additional_repositories: https://imran-aifi.github.io/drat
biocViews: Data analysis, Chromatin Accessibility, Single cell, scATAC,
        Software, Visualization
VignetteBuilder: knitr
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2022-12-06 08:10:54 UTC; imran.mcgrath
Author: Samir Rachid Zaim [aut, ctb],
  Mark-Phillip Pebworth [aut, ctb],
  Imran McGrath [aut, cre],
  Lauren Okada [aut, ctb],
  Xiaojun Li [aut, ctb]
Repository: CRAN
Date/Publication: 2022-12-06 13:42:38 UTC
Built: R 4.3.0; ; 2023-04-11 03:17:44 UTC; unix
