Package: orthogene 1.11.0

Brian Schilder

orthogene: Interspecies gene mapping

`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]

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orthogene.pdf |orthogene.html✨
orthogene/json (API)
NEWS

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

Peer review:

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

Datasets:

On BioConductor:orthogene-1.11.0(bioc 3.20)orthogene-1.10.0(bioc 3.19)

geneticscomparativegenomicspreprocessingphylogeneticstranscriptomicsgeneexpressionanimal-modelsbioconductorbioconductor-packagebioinformaticsbiomedicinecomparative-genomicsevolutionary-biologygenesgenomicsontologiestranslational-research

14 exports 40 stars 7.41 score 143 dependencies 1 dependents 24 scripts 513 downloads

Last updated 5 months agofrom:37712f29cc. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 28 2024
R-4.5-winNOTESep 28 2024
R-4.5-linuxNOTESep 28 2024
R-4.4-winNOTESep 28 2024
R-4.4-macNOTESep 28 2024
R-4.3-winOKSep 28 2024
R-4.3-macOKSep 28 2024

Exports:aggregate_mapped_genesall_genesall_speciesconvert_orthologscreate_backgroundformat_speciesget_silhouettesinfer_speciesmap_genesmap_orthologsmap_speciesplot_orthotreeprepare_treereport_orthologs

Dependencies:abindapeaplotaskpassbabelgenebackportsbase64encBiocGenericsbitbit64bitopsbootbroombslibcachemcarcarDataclicliprcolorspacecorrplotcowplotcpp11crayoncrosstalkcurldata.tableDelayedArrayDerivdigestdoBydplyrevaluatefansifarverfastmapfontawesomeFormulafsgenericsggfunggplot2ggplotifyggpubrggrepelggsciggsignifggtreegluegprofiler2gridExtragridGraphicsgrrgtablehighrhmshomologenehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivopensslpatchworkpbkrtestpillarpkgconfigplotlyplyrpolynomprettyunitsprogresspromisespurrrquantregR.cacheR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRCurlreadrrepmisrlangrmarkdownrstatixS4ArraysS4VectorssassscalesSparseArraySparseMstringistringrsurvivalsystibbletidyrtidyselecttidytreetinytextreeiotzdbutf8vctrsviridisLitevroomwithrxfunXVectoryamlyulab.utilszlibbioc

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 Sep 28 2024.

Last update: 2022-02-20
Started: 2021-10-27

Infer species

Author: Brian M. Schilder

Rendered frominfer_species.Rmdusingknitr::rmarkdownon Sep 28 2024.

Last update: 2021-10-29
Started: 2021-10-20

orthogene: Getting Started

Author: Brian M. Schilder

Rendered fromorthogene.Rmdusingknitr::rmarkdownon Sep 28 2024.

Last update: 2022-05-20
Started: 2021-08-25