Package: orthogene 1.13.0
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:
orthogene_1.13.0.tar.gz
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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')) |
Bug tracker:https://github.com/neurogenomics/orthogene/issues
- exp_mouse - Gene expression data: mouse
- exp_mouse_enst - Transcript expression data: mouse
On BioConductor:orthogene-1.11.0(bioc 3.20)orthogene-1.10.0(bioc 3.19)
geneticscomparativegenomicspreprocessingphylogeneticstranscriptomicsgeneexpressionanimal-modelsbioconductorbioconductor-packagebioinformaticsbiomedicinecomparative-genomicsevolutionary-biologygenesgenomicsontologiestranslational-research
Last updated 26 days agofrom:cd1c983cb5. Checks:OK: 1 NOTE: 1 ERROR: 5. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | ERROR | Oct 30 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | ERROR | Oct 30 2024 |
| R-4.4-mac | ERROR | Oct 30 2024 |
| R-4.3-win | ERROR | Oct 30 2024 |
| R-4.3-mac | ERROR | Oct 30 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
Rendered fromdocker.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2022-02-20
Started: 2021-10-27
Infer species
Rendered frominfer_species.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2021-10-29
Started: 2021-10-20
orthogene: Getting Started
Rendered fromorthogene.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2022-05-20
Started: 2021-08-25
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 'orthogene': Interspecies gene mapping | orthogene-package orthogene |
| Aggregate/expand a gene matrix by gene mappings | aggregate_mapped_genes |
| Get all genes | all_genes |
| All species | all_species |
| Map genes from one species to another | convert_orthologs |
| Create gene background | create_background |
| Gene expression data: mouse | exp_mouse |
| Transcript expression data: mouse | exp_mouse_enst |
| Format species names | format_species |
| Get silhouettes | get_silhouettes |
| gconvert namespaces | gprofiler_namespace |
| Reference organisms | gprofiler_orgs |
| Infer species from gene names | infer_species |
| Map genes | map_genes |
| Map orthologs | map_orthologs |
| Standardise species names | map_species |
| Create a phylogenetic tree of shared orthologs | plot_orthotree |
| Prepare a phylogenetic tree | prepare_tree |
| Report orthologs | report_orthologs |
