mitch
This is the development version of mitch; for the stable release version, see mitch.
Multi-Contrast Gene Set Enrichment Analysis
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Mark Ziemann <mark.ziemann at gmail.com>
citation("mitch")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DNAMethylation, DifferentialExpression, Epigenetics, GeneExpression, GeneSetEnrichment, MethylationArray, Proteomics, Reactome, SingleCell, Software, Transcriptomics |
| Version | 1.19.3 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 years) |
| License | CC BY-SA 4.0 + file LICENSE |
| Depends | R (>= 4.4) |
| 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 |
| Bug Reports | https://github.com/markziemann/mitch |
See More
| Suggests | stringi, testthat (>= 2.1.0), HGNChelper, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | mitch_1.19.3.tar.gz |
| Windows Binary (x86_64) | mitch_1.19.3.zip |
| macOS Binary (x86_64) | mitch_1.19.3.tgz |
| macOS Binary (arm64) | mitch_1.19.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/mitch |
| Source Repository (Developer Access) | git clone [email protected]:packages/mitch |
| Bioc Package Browser | https://code.bioconductor.org/browse/mitch/ |
| Package Short Url | https://bioconductor.org/packages/mitch/ |
| Package Downloads Report | Download Stats |