Package: compartmap
Type: Package
Title: Higher-order chromatin domain inference in single cells from
        scRNA-seq and scATAC-seq
Description: Compartmap performs direct inference of higher-order chromatin
    from scRNA-seq and scATAC-seq. This package implements a James-Stein estimator
    for computing single-cell level higher-order chromatin domains. Further, we
    utilize random matrix theory as a method to de-noise correlation matrices to
    achieve a similar "plaid-like" patterning as observed in Hi-C and scHi-C data.
Version: 1.22.0
Date: 2021-05-03
Authors@R: c(person("Benjamin", "Johnson", role = c("aut", "cre"),
                    email = "ben.johnson@vai.org",),
             person("Tim", "Triche", role = c("aut")),
	     person("Hui", "Shen", role = c("aut")),
             person("Kasper", "Hansen", role = c("aut")),
             person("Jean-Philippe", "Fortin", role = c("aut")))
URL: https://github.com/biobenkj/compartmap
BugReports: https://github.com/biobenkj/compartmap/issues
Encoding: UTF-8
License: GPL-3 + file LICENSE
biocViews: Genetics, Epigenetics, ATACSeq, RNASeq, SingleCell
Depends: R (>= 4.1.0), SummarizedExperiment, RaggedExperiment,
        BiocSingular, HDF5Array
Imports: GenomicRanges, parallel, grid, ggplot2, reshape2, scales,
        DelayedArray, rtracklayer, DelayedMatrixStats, Matrix, RMTstat
Suggests: covr, testthat, knitr, Rcpp, rmarkdown, markdown
RoxygenNote: 7.1.1
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
PackageStatus: Deprecated
git_url: https://git.bioconductor.org/packages/compartmap
git_branch: RELEASE_3_19
git_last_commit: 8d4beb1
git_last_commit_date: 2024-04-30
Repository: Bioconductor 3.19
Date/Publication: 2024-05-01
NeedsCompilation: no
Packaged: 2024-05-01 21:57:47 UTC; biocbuild
Author: Benjamin Johnson [aut, cre],
  Tim Triche [aut],
  Hui Shen [aut],
  Kasper Hansen [aut],
  Jean-Philippe Fortin [aut]
Maintainer: Benjamin Johnson <ben.johnson@vai.org>
Built: R 4.4.0; ; 2024-05-02 12:37:57 UTC; windows
