Package: mitch 1.24.0

Mark Ziemann

mitch: Multi-Contrast Gene Set Enrichment Analysis

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.

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

mitch_1.24.0.tar.gz
mitch_1.24.0.zip(r-4.7-any)mitch_1.24.0.zip(r-4.6-any)mitch_1.24.0.zip(r-4.5-any)
mitch_1.24.0.tgz(r-4.6-any)mitch_1.24.0.tgz(r-4.5-any)
mitch_1.24.0.tar.gz(r-4.7-any)mitch_1.24.0.tar.gz(r-4.6-any)
mitch_1.24.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mitch/json (API)

# Install 'mitch' in R:
install.packages('mitch', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/markziemann/mitch/issues

Datasets:

On BioConductor:mitch-1.25.0(bioc 3.24)mitch-1.24.0(bioc 3.23)

geneexpressiongenesetenrichmentsinglecelltranscriptomicsepigeneticsproteomicsdifferentialexpressionreactomednamethylationmethylationarraydataimportgene-regulationgene-seq-analysispathway-analysis

6.61 score 18 stars 19 scripts 3 mentions 7 exports 94 dependencies

Last updated from:1235d24581 (on RELEASE_3_23). Checks:1 WARNING, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING411
linux-devel-x86_64OK508
source / vignettesOK586
linux-release-x86_64OK554
macos-release-arm64OK345
macos-oldrel-arm64OK292
windows-develOK1889
windows-releaseOK1905
windows-oldrelOK1887
wasm-releaseOK418

Exports:gmt_importmitch_calcmitch_importmitch_plotsmitch_reportnetwork_genesnetworkplot

Dependencies:backportsbase64encbeeswarmbitopsbroombslibcachemcaToolsclicodacommonmarkcorrplotcountrycodecpp11crayondigestdplyrecharts4revaluatefarverfastmapfontawesomeforcatsfsgenericsGGallyggplot2ggstatsgluegplotsgridExtragtablegtoolshighrhmshtmltoolshtmlwidgetshttpuvisobandjquerylibjsonlitekableExtraKernSmoothknitrlabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemimenetworkotelpatchworkpillarpkgconfigplyrprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownrstudioapiS7sassscalesshinysourcetoolsstatnet.commonstringistringrsvglitesystemfontstextshapingtibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxml2xtableyaml

Applying mitch to pathway analysis of Infinium Methylation array data
Background | Requirements | Gene sets | Probe gene relationship for HM450K array data | Update deprecated gene symbols | Importing profiling data | Calculating enrichment | Downstream presentation | Probe gene relationship for EPIC array data | Session Info
Rendered frominfiniumMethArrayWorkflow.Rmdusingknitr::rmarkdown

Last update: 2025-03-31
Started: 2024-02-19

mitch Workflow
Background | Importing gene sets | Importing profiling data | Calculating enrichment | Generate a HTML report | Generate high resolution plots | Network plot | Session Info
Rendered frommitchWorkflow.Rmdusingknitr::rmarkdown

Last update: 2025-03-31
Started: 2019-10-06