Package: mitology 1.5.0

Stefania Pirrotta

mitology: Study of mitochondrial activity from RNA-seq data

mitology allows to study the mitochondrial activity throught high-throughput RNA-seq data. It is based on a collection of genes whose proteins localize in to the mitochondria. From these, mitology provides a reorganization of the pathways related to mitochondria activity from Reactome and Gene Ontology. Further a ready-to-use implementation of MitoCarta3.0 pathways is included.

Authors:Stefania Pirrotta [cre, aut], Enrica Calura [aut, fnd]

mitology_1.5.0.tar.gz
mitology_1.5.0.zip(r-4.7)mitology_1.5.0.zip(r-4.6)mitology_1.5.0.zip(r-4.5)
mitology_1.5.0.tgz(r-4.6-any)mitology_1.5.0.tgz(r-4.5-any)
mitology_1.5.0.tar.gz(r-4.7-any)mitology_1.5.0.tar.gz(r-4.6-any)
mitology_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mitology/json (API)

# Install 'mitology' in R:

install.packages('mitology', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/caluralab/mitology/issues

Datasets:

MitoGenesDB - Mitochondrial genes
ovse - Example expression data.

On BioConductor:mitology-1.5.0(bioc 3.24)mitology-1.4.0(bioc 3.23)

geneexpression rnaseq visualization singlecell spatial pathways reactome go

4.60 score 2 stars 5 scripts 291 downloads 6 exports 147 dependencies

Last updated from:6b9bf1537b. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	317
linux-devel-x86_64	OK	521
source / vignettes	OK	455
linux-release-x86_64	OK	467
macos-release-arm64	OK	250
macos-oldrel-arm64	OK	278
windows-devel	OK	349
windows-release	OK	336
windows-oldrel	OK	383
wasm-release	OK	301

Exports:enrichMito getGeneSets gseaMito mitoHeatmap mitoTreeHeatmap mitoTreePoint

Dependencies:aisdk AnnotationDbi ape aplot askpass base64enc Biobase BiocGenerics Biostrings bit bit64 blob bslib cachem callr circlize cli clue cluster clusterProfiler codetools colorspace ComplexHeatmap cpp11 crayon curl DBI digest dir.expiry doParallel DOSE dplyr enrichit enrichplot evaluate farver fastmap filelock fontawesome fontBitstreamVera fontLiberation fontquiver foreach fs gdtools generics GetoptLong ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggraph ggrepel ggtangle ggtree GlobalOptions glue GO.db GOSemSim graph graphite graphlayouts gridExtra gridGraphics gson gtable highr htmltools htmlwidgets httr httr2 igraph IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lattice lazyeval lifecycle magrittr MASS Matrix matrixStats memoise mime nlme openssl org.Hs.eg.db otel patchwork pillar pkgconfig plyr png polyclip processx ps purrr qvalue R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reactome.db ReactomePA reshape2 rjson rlang rmarkdown RSQLite S4Vectors S7 sass scales scatterpie Seqinfo shape stringi stringr sys systemfonts tibble tidydr tidygraph tidyr tidyselect tidytree tinytex treeio tweenr utf8 vctrs viridis viridisLite withr xfun XVector yaml yulab.utils

mitology vignette

Rendered frommitology.Rmdusingknitr::rmarkdown

Last update: 2025-10-20
Started: 2021-05-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Mitochondrial Enrichment Analysis of a gene list.	enrichMito
Get the mitochondrial gene sets	getGeneSets
Mitochondrial GSEA of a gene list.	gseaMito
Mitochondrial genes	MitoGenesDB
Heatmap of mitochondrial gene sets.	mitoHeatmap
Circular heatmap on mitochondrial gene set tree.	mitoTreeHeatmap
Circular dotplot on mitochondrial gene set tree.	mitoTreePoint
Example expression data.	ovse