orthogene
This is the released version of orthogene; for the devel version, see orthogene.
Gene mapping made easy
Bioconductor version: Release (3.23)
`orthogene` is an R package for easy mapping of orthologous genes across hundreds of species. It pulls up-to-date gene ortholog mappings across **700+ organisms**. It also provides various utility functions to aggregate/expand common objects (e.g. data.frames, gene expression matrices, lists) using **1:1**, **many:1**, **1:many** or **many:many** gene mappings, both within- and between-species.
Author: Brian Schilder [cre, fnd]
Maintainer: Brian Schilder <brian_schilder at alumni.brown.edu>
citation("orthogene")):
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("orthogene")
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("orthogene")| docker | HTML | R Script |
| Infer species | HTML | R Script |
| orthogene | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ComparativeGenomics, GeneExpression, Genetics, Phylogenetics, Preprocessing, Software, Transcriptomics |
| Version | 1.18.1 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 years) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | dplyr, methods, stats, utils, Matrix, jsonlite, homologene, gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr, patchwork, DelayedArray, repmis, ggtree, tools, magrittr |
| System Requirements | |
| URL | https://github.com/neurogenomics/orthogene |
| Bug Reports | https://github.com/neurogenomics/orthogene/issues |
See More
| Suggests | remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | BulkSignalR, EWCE |
| Suggests Me | sparrow |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | orthogene_1.18.1.tar.gz |
| Windows Binary (x86_64) | orthogene_1.18.1.zip |
| macOS Binary (big-sur-x86_64) | orthogene_1.18.1.tgz |
| macOS Binary (sonoma-arm64) | orthogene_1.18.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/orthogene |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/orthogene |
| Bioc Package Browser | https://code.bioconductor.org/browse/orthogene/ |
| Package Short Url | https://bioconductor.org/packages/orthogene/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |