Package: orthogene 1.19.3

Brian Schilder

orthogene: Gene mapping made easy

`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.

Authors:Brian Schilder [cre, fnd]

orthogene_1.19.3.tar.gz
orthogene_1.19.3.zip(r-4.7)orthogene_1.19.3.zip(r-4.6)orthogene_1.19.3.zip(r-4.5)
orthogene_1.19.3.tgz(r-4.6-any)orthogene_1.19.3.tgz(r-4.5-any)
orthogene_1.19.3.tar.gz(r-4.7-any)orthogene_1.19.3.tar.gz(r-4.6-any)
orthogene_1.19.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
orthogene/json (API)
NEWS

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

Bug tracker:https://github.com/neurogenomics/orthogene/issues

Datasets:

On BioConductor:orthogene-1.19.3(bioc 3.24)orthogene-1.18.1(bioc 3.23)

geneticscomparativegenomicspreprocessingphylogeneticstranscriptomicsgeneexpressionanimal-modelsbioconductorbioconductor-packagebioinformaticsbiomedicinecomparative-genomicsevolutionary-biologygenesgenomicsontologiestranslational-research

9.13 score 56 stars 3 packages 82 scripts 1.0k downloads 14 exports 157 dependencies

Last updated from:9d34d75e09. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE221
linux-devel-x86_64OK1137
source / vignettesOK283
linux-release-x86_64OK1102
macos-release-arm64OK622
macos-oldrel-arm64OK650
windows-develOK896
windows-releaseOK735
windows-oldrelOK806
wasm-releaseOK201

Exports:aggregate_mapped_genesall_genesall_speciesconvert_orthologscreate_backgroundformat_speciesget_silhouettesinfer_speciesmap_genesmap_orthologsmap_speciesplot_orthotreeprepare_treereport_orthologs

Dependencies:abindapeaplotaskpassbabelgenebackportsbase64encBiocGenericsbitbit64bitopsbootbroombslibcachemcarcarDataclicliprcolorspacecorrplotcowplotcpp11crayoncrosstalkcurldata.tableDelayedArrayDerivdigestdoBydplyrevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverforecastFormulafracdifffsgdtoolsgenericsggfunggiraphggplot2ggplotifyggpubrggrepelggsciggsignifggtreegluegprofiler2gridExtragridGraphicsgtablehighrhmshomologenehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrnlmenloptrnnetnumDerivopensslotelpatchworkpbkrtestpillarpkgconfigplotlyplyrpolynomprettyunitsprogresspromisespurrrquantregR.cacheR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreadrreformulasrepmisrlangrmarkdownrstatixS4ArraysS4VectorsS7sassscalesSparseArraySparseMstringistringrsurvivalsyssystemfontstibbletidyrtidyselecttidytreetimeDatetinytextreeiotzdburcautf8vctrsviridisLitevroomwithrxfunXVectoryamlyulab.utilszoo

Docker/Singularity Containers

Authors: `r auths <- eval(parse(text = gsub("person","c",read.dcf("../DESCRIPTION", fields = "Authors@R"))));paste(auths[names(auths)=="given"],auths[names(auths)=="family"], collapse = ", ")`

Rendered fromdocker.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2023-12-21
Started: 2021-10-27

Infer species

Author: Brian M. Schilder

Rendered frominfer_species.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-01-03
Started: 2021-10-20

orthogene: Getting Started

Author: Brian M. Schilder

Rendered fromorthogene.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-01-03
Started: 2021-08-25