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mitch

This is the development version of mitch; for the stable release version, see mitch.

Multi-Contrast Gene Set Enrichment Analysis


Bioconductor version: Development (3.20)

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.

Author: Mark Ziemann [aut, cre, cph] , Antony Kaspi [aut, cph]

Maintainer: Mark Ziemann <mark.ziemann at gmail.com>

Citation (from within R, enter citation("mitch")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("mitch")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("mitch")
Applying mitch to pathway analysis of Infinium Methylation array data HTML R Script
mitch Workflow HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DNAMethylation, DifferentialExpression, Epigenetics, GeneExpression, GeneSetEnrichment, MethylationArray, Proteomics, Reactome, SingleCell, Software, Transcriptomics
Version 1.17.1
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License CC BY-SA 4.0 + file LICENSE
Depends R (>= 4.3)
Imports stats, grDevices, graphics, utils, MASS, plyr, reshape2, parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2, gplots, beeswarm, echarts4r, kableExtra
System Requirements
URL https://github.com/markziemann/mitch
See More
Suggests stringi, testthat (>= 2.1.0), HGNChelper, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package mitch_1.17.1.tar.gz
Windows Binary mitch_1.17.1.zip (64-bit only)
macOS Binary (x86_64) mitch_1.17.1.tgz
macOS Binary (arm64) mitch_1.17.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/mitch
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/mitch
Bioc Package Browser https://code.bioconductor.org/browse/mitch/
Package Short Url https://bioconductor.org/packages/mitch/
Package Downloads Report Download Stats