mitch

DOI: 10.18129/B9.bioc.mitch    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see mitch.

Multi-Contrast Gene Set Enrichment Analysis

Bioconductor version: 3.15

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. 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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	mitch Workflow
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, Epigenetics, GeneExpression, GeneSetEnrichment, Proteomics, Reactome, SingleCell, Software, Transcriptomics
Version	1.8.0
In Bioconductor since	BioC 3.11 (R-4.0) (2.5 years)
License	CC BY-SA 4.0 + file LICENSE
Depends	R (>= 4.0)
Imports	stats, grDevices, graphics, utils, MASS, plyr, reshape2, parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2, gplots, beeswarm, echarts4r
LinkingTo
Suggests	stringi, testthat (>= 2.1.0)
SystemRequirements
Enhances
URL	https://github.com/markziemann/mitch
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	mitch_1.8.0.tar.gz
Windows Binary	mitch_1.8.0.zip
macOS Binary (x86_64)	mitch_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mitch
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mitch
Package Short Url	https://bioconductor.org/packages/mitch/
Package Downloads Report	Download Stats