mitology
This is the released version of mitology; for the devel version, see mitology.
Study of mitochondrial activity from RNA-seq data
Bioconductor version: Release (3.23)
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.
Author: Stefania Pirrotta [cre, aut]
, Enrica Calura [aut, fnd]
Maintainer: Stefania Pirrotta <stefania.pirrotta at unipd.it>
citation("mitology")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("mitology")
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("mitology")| mitology vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GO, GeneExpression, Pathways, RNASeq, Reactome, SingleCell, Software, Spatial, Visualization |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | AGPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | AnnotationDbi, ape, circlize, clusterProfiler, ComplexHeatmap, ggplot2, ggtree, magrittr, org.Hs.eg.db, ReactomePA, scales |
| System Requirements | |
| URL | https://github.com/CaluraLab/mitology |
| Bug Reports | https://github.com/CaluraLab/mitology/issues |
See More
| Suggests | Biobase, BiocStyle, GSVA, methods, rmarkdown, knitr, SummarizedExperiment, testthat |
| 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 | mitology_1.4.0.tar.gz |
| Windows Binary (x86_64) | mitology_1.4.0.zip |
| macOS Binary (big-sur-x86_64) | mitology_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | mitology_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/mitology |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/mitology |
| Bioc Package Browser | https://code.bioconductor.org/browse/mitology/ |
| Package Short Url | https://bioconductor.org/packages/mitology/ |
| Package Downloads Report | Download Stats |