Package: mitch
Title: Multi-Contrast Gene Set Enrichment Analysis
Version: 1.22.0
Authors@R: c(
    person(given = "Mark",
        family = "Ziemann",
        role = c("aut","cre","cph"),
        email = "mark.ziemann@gmail.com",
        comment = c(ORCID="0000-0002-7688-6974")),
    person(given="Antony",
        family="Kaspi",
        role = c("aut","cph"))
    )
Description: mitch is an R package for multi-contrast enrichment
        analysis. At it’s heart, it uses a rank-MANOVA based
        statistical approach to detect sets of genes that exhibit
        enrichment in the multidimensional space as compared to the
        background. The rank-MANOVA concept dates to work by Cox and
        Mann (https://doi.org/10.1186/1471-2105-13-S16-S12). mitch is
        useful for pathway analysis of profiling studies with one, two
        or more contrasts, or in studies with multiple omics profiling,
        for example proteomic, transcriptomic, epigenomic analysis of
        the same samples. mitch is perfectly suited for pathway level
        differential analysis of scRNA-seq data. We have an established
        routine for pathway enrichment of Infinium Methylation Array
        data (see vignette). The main strengths of mitch are that it
        can import datasets easily from many upstream tools and has
        advanced plotting features to visualise these enrichments.
Depends: R (>= 4.4)
Suggests: stringi, testthat (>= 2.1.0), HGNChelper,
        IlluminaHumanMethylation450kanno.ilmn12.hg19,
        IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Imports: stats, grDevices, graphics, utils, MASS, plyr, reshape2,
        parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2,
        gplots, beeswarm, echarts4r, kableExtra, dplyr, network
License: CC BY-SA 4.0 + file LICENSE
Encoding: UTF-8
URL: https://github.com/markziemann/mitch
BugReports: https://github.com/markziemann/mitch
LazyData: false
RoxygenNote: 7.3.2
biocViews: GeneExpression, GeneSetEnrichment, SingleCell,
        Transcriptomics, Epigenetics, Proteomics,
        DifferentialExpression, Reactome, DNAMethylation,
        MethylationArray, DataImport
VignetteBuilder: knitr
Config/pak/sysreqs: libfontconfig1-dev libfreetype6-dev libfribidi-dev
        make libharfbuzz-dev libicu-dev libpng-dev libxml2-dev
        libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:55:52 UTC
RemoteUrl: https://github.com/bioc/mitch
RemoteRef: RELEASE_3_22
RemoteSha: cae4ecbe0119cb8c53bf9022c5eade15416b5c53
NeedsCompilation: no
Packaged: 2025-11-13 07:41:39 UTC; root
Author: Mark Ziemann [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-7688-6974>),
  Antony Kaspi [aut, cph]
Maintainer: Mark Ziemann <mark.ziemann@gmail.com>
Built: R 4.5.2; ; 2025-11-13 07:45:33 UTC; windows
