{"id":32176018,"url":"https://github.com/oganm/homologene","last_synced_at":"2026-02-18T22:02:25.409Z","repository":{"id":39458247,"uuid":"41837020","full_name":"oganm/homologene","owner":"oganm","description":":mouse: :left_right_arrow: :couple: An r package that works as a wrapper to homologene","archived":false,"fork":false,"pushed_at":"2023-11-02T01:06:31.000Z","size":323515,"stargazers_count":47,"open_issues_count":5,"forks_count":5,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-12-08T01:22:59.051Z","etag":null,"topics":["bioinformatics","homologene","mancarci-2017","ncbi-taxonomy","ogan-bio","species","wrapper"],"latest_commit_sha":null,"homepage":"https://oganm.github.io/homologene/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/oganm.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2015-09-03T01:50:05.000Z","updated_at":"2025-12-01T07:52:03.000Z","dependencies_parsed_at":"2022-08-09T14:49:11.898Z","dependency_job_id":"8ad04dbf-d71f-4f2a-846c-3fa1da856cea","html_url":"https://github.com/oganm/homologene","commit_stats":{"total_commits":288,"total_committers":4,"mean_commits":72.0,"dds":0.06944444444444442,"last_synced_commit":"9a9f99c4b596ccdd05a1ea1d7f62323bffb3b721"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/oganm/homologene","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oganm%2Fhomologene","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oganm%2Fhomologene/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oganm%2Fhomologene/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oganm%2Fhomologene/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/oganm","download_url":"https://codeload.github.com/oganm/homologene/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oganm%2Fhomologene/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29596330,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-18T20:59:56.587Z","status":"ssl_error","status_checked_at":"2026-02-18T20:58:41.434Z","response_time":162,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","homologene","mancarci-2017","ncbi-taxonomy","ogan-bio","species","wrapper"],"created_at":"2025-10-21T19:53:11.873Z","updated_at":"2026-02-18T22:02:25.403Z","avatar_url":"https://github.com/oganm.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n# homologene\n\n[![Build\nStatus](https://travis-ci.org/oganm/homologene.svg?branch=master)](https://travis-ci.org/oganm/homologene)\n[![codecov](https://codecov.io/gh/oganm/homologene/branch/master/graph/badge.svg)](https://codecov.io/gh/oganm/homologene)\n[![](https://www.r-pkg.org/badges/version/homologene?color=#32BD36)](https://cran.r-project.org/package=homologene)\n[![](https://img.shields.io/badge/devel%20version-1.7.68.23.10.31-blue.svg)](https://github.com/oganm/homologene)\n\nAn r package that works as a wrapper to homologene\n\nAvailable species are\n\n``` r\nhomologene::taxData\n```\n\n ## tax_id name_txt\n ## 1 10090 Mus musculus\n ## 2 10116 Rattus norvegicus\n ## 3 28985 Kluyveromyces lactis\n ## 4 318829 Magnaporthe oryzae\n ## 5 33169 Eremothecium gossypii\n ## 6 3702 Arabidopsis thaliana\n ## 7 4530 Oryza sativa\n ## 8 4896 Schizosaccharomyces pombe\n ## 9 4932 Saccharomyces cerevisiae\n ## 10 5141 Neurospora crassa\n ## 11 6239 Caenorhabditis elegans\n ## 12 7165 Anopheles gambiae\n ## 13 7227 Drosophila melanogaster\n ## 14 7955 Danio rerio\n ## 15 8364 Xenopus (Silurana) tropicalis\n ## 16 9031 Gallus gallus\n ## 17 9544 Macaca mulatta\n ## 18 9598 Pan troglodytes\n ## 19 9606 Homo sapiens\n ## 20 9615 Canis lupus familiaris\n ## 21 9913 Bos taurus\n\n# Installation\n\n``` r\ninstall.packages('homologene')\n```\n\nor\n\n``` r\ndevtools::install_github('oganm/homologene')\n```\n\n# Usage\n\nBasic homologene function requires a list of gene symbols or NCBI ids,\nand an `inTax` and an `outTax`. In this example, `inTax` is the taxon id\nof *mus musculus* while `outTax` is for humans.\n\n``` r\nhomologene(c('Eno2','Mog'), inTax = 10090, outTax = 9606)\n```\n\n ## 10090 9606 10090_ID 9606_ID\n ## 1 Eno2 ENO2 13807 2026\n ## 2 Mog MOG 17441 4340\n\n``` r\nhomologene(c('Eno2','17441'), inTax = 10090, outTax = 9606)\n```\n\n ## 10090 9606 10090_ID 9606_ID\n ## 1 Eno2 ENO2 13807 2026\n ## 2 Mog MOG 17441 4340\n\nFor mouse and humans two convenience functions exist that removes the\nneed to provide taxonomic identifiers. Note that the column names are\nnot the same as the `homologene` output.\n\n``` r\nmouse2human(c('Eno2','Mog'))\n```\n\n ## mouseGene humanGene mouseID humanID\n ## 1 Eno2 ENO2 13807 2026\n ## 2 Mog MOG 17441 4340\n\n``` r\nhuman2mouse(c('ENO2','MOG','GZMH'))\n```\n\n ## humanGene mouseGene humanID mouseID\n ## 1 ENO2 Eno2 2026 13807\n ## 2 MOG Mog 4340 17441\n ## 3 GZMH Gzmd 2999 14941\n ## 4 GZMH Gzme 2999 14942\n ## 5 GZMH Gzmg 2999 14944\n ## 6 GZMH Gzmf 2999 14943\n\n# homologeneData2\n\nOriginal homologene database has not been updated since 2014. This\npackage also includes an updated version of the homologene database that\nreplaces gene symbols and identifiers with the their latest version. For\nthe procedure followed for updating, see [this blog\npost](https://oganm.com/homologene-update/) and/or see the [processing\ncode](R/updateHomologene.R).\n\nUsing the updated version can help you match genes that cannot matched\ndue to out of date annotations.\n\n``` r\nmouse2human(c('Mesd',\n 'Trp53rka',\n 'Cstdc4',\n 'Ifit3b'))\n```\n\n ## [1] mouseGene humanGene mouseID humanID \n ## \u003c0 rows\u003e (or 0-length row.names)\n\n``` r\nmouse2human(c('Mesd',\n 'Trp53rka',\n 'Cstdc4',\n 'Ifit3b'),\n db = homologeneData2)\n```\n\n ## mouseGene humanGene mouseID humanID\n ## 1 Mesd MESD 67943 23184\n ## 2 Trp53rka TP53RK 381406 112858\n ## 3 Cstdc4 CSTA 433016 1475\n ## 4 Ifit3b IFIT3 667370 3437\n\nThe `homologeneData2` object that comes with the GitHub version of this\npackage is updated weekly but if you are using the CRAN version and want\nthe latest annotations, or if you want to keep a frozen version\nhomologene, you can use the `updateHomologene` function.\n\n``` r\nhomologeneDataVeryNew = updateHomologene() # update the homologene database with the latest identifiers\n\nmouse2human(c('Mesd',\n 'Trp53rka',\n 'Cstdc4',\n 'Ifit3b'),\n db = homologeneDataVeryNew)\n```\n\n# Gene ID syncronization\n\nThe package also includes functions that were used to create the\n`homologeneData2`, for updating outdated gene symbols and identifiers.\n\n``` r\nlibrary(dplyr)\n\ngene_history = getGeneHistory()\noldIds = c(4340964, 4349034, 4332470, 4334151, 4323831)\nnewIds = updateIDs(oldIds,gene_history)\nprint(newIds)\n```\n\n ## [1] \"9267698\" \"4349033\" \"4332468\" \"4334150\" \"4324017\"\n\n``` r\n# get the latest gene symbols for the ids\n\ngene_info = getGeneInfo()\n\ngene_info %\u003e%\n dplyr::filter(GeneID %in% as.integer(newIds)) # faster to match integers\n```\n\n ## # A tibble: 5 × 3\n ## tax_id GeneID Symbol \n ## \u003cint\u003e \u003cint\u003e \u003cchr\u003e \n ## 1 39947 4324017 LOC4324017\n ## 2 39947 4332468 SPO11-3 \n ## 3 39947 4334150 LOC4334150\n ## 4 39947 4349033 LOC4349033\n ## 5 39947 9267698 LOC9267698\n\n# Querying DIOPT\n\nInstead of using just homologene, one can also make queries into the\n[DIOPT database](https://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl).\nDiopt uses multiple databases to find gene homolog/orthologues. Note\nthat this function has a `delay` parameter that is set to 10 seconds by\ndefault. This was done to obey the `robots.txt` of their website.\n\n``` r\ndiopt(c('GZMH'),inTax = 9606, outTax = 10090) %\u003e% \n knitr::kable()\n```\n\n| Input Order | Search Term | Human GeneID | HGNCID | Human Symbol | Species 2 | Mouse GeneID | Mouse Species Gene ID | Mouse Symbol | Ensmbl ID (link HPA) | DIOPT Score | Weighted Score | Rank | Best Score | Best Score Reverse | Prediction Derived From | Alignment \u0026 Scores | Feedback | Gene Details |\n|------------:|:------------|-------------:|-------:|:-------------|:----------|-------------:|----------------------:|:-------------|:---------------------|------------:|---------------:|:---------|:-----------|:-------------------|:-------------------------------------------------------|:-------------------|:---------|:-----------------------------------------|\n| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 14944 | 109253 | Gzmg | NA | 6 | 5.87 | high | Yes | Yes | eggNOG, Homologene, Isobase, OrthoDB, Panther, Phylome | NA | Add | G2F details (Gzmg) DRscDB Data: (Gzmg) |\n| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 14939 | 109267 | Gzmb | NA | 6 | 5.85 | moderate | Yes | No | eggNOG, OrthoDB, orthoMCL, Panther, Phylome, RoundUp | NA | Add | G2F details (Gzmb) DRscDB Data: (Gzmb) |\n| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 245839 | 2675494 | Gzmn | NA | 5 | 4.93 | moderate | No | No | eggNOG, OMA, OrthoDB, Panther, Phylome | NA | Add | G2F details (Gzmn) DRscDB Data: (Gzmn) |\n| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 14940 | 109256 | Gzmc | NA | 5 | 4.93 | moderate | No | No | eggNOG, OMA, OrthoDB, Panther, Phylome | NA | Add | G2F details (Gzmc) DRscDB Data: (Gzmc) |\n| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 14941 | 109255 | Gzmd | NA | 5 | 4.92 | moderate | No | No | eggNOG, Homologene, OrthoDB, Panther, Phylome | NA | Add | G2F details (Gzmd) DRscDB Data: (Gzmd) |\n| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 14943 | 109254 | Gzmf | NA | 5 | 4.92 | moderate | No | No | eggNOG, Homologene, OrthoDB, Panther, Phylome | NA | Add | G2F details (Gzmf) DRscDB Data: (Gzmf) |\n| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 14942 | 109265 | Gzme | NA | 5 | 4.92 | moderate | No | No | eggNOG, Homologene, OrthoDB, Panther, Phylome | NA | Add | G2F details (Gzme) DRscDB Data: (Gzme) |\n| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 17231 | 1261780 | Mcpt8 | NA | 4 | 3.97 | moderate | No | No | eggNOG, OrthoDB, Panther, TreeFam | NA | Add | G2F details (Mcpt8) DRscDB Data: (Mcpt8) |\n| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 13035 | 88563 | Ctsg | NA | 2 | 1.91 | low | No | No | eggNOG, OrthoDB | NA | Add | G2F details (Ctsg) DRscDB Data: (Ctsg) |\n| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 17228 | 96941 | Cma1 | NA | 2 | 1.91 | low | No | No | eggNOG, OrthoDB | NA | Add | G2F details (Cma1) DRscDB Data: (Cma1) |\n| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 14938 | 109266 | Gzma | NA | 1 | 1.03 | low | No | No | RoundUp | NA | Add | G2F details (Gzma) DRscDB Data: (Gzma) |\n| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 17232 | 1194491 | Mcpt9 | NA | 1 | 1.01 | low | No | Yes | OrthoDB | NA | Add | G2F details (Mcpt9) DRscDB Data: (Mcpt9) |\n| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 17225 | 96938 | Mcpt2 | NA | 1 | 1.01 | low | No | Yes | OrthoDB | NA | Add | G2F details (Mcpt2) DRscDB Data: (Mcpt2) |\n| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 17224 | 96937 | Mcpt1 | NA | 1 | 1.01 | low | No | Yes | OrthoDB | NA | Add | G2F details (Mcpt1) DRscDB Data: (Mcpt1) |\n| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 545055 | 88426 | Cma2 | NA | 1 | 1.01 | low | No | Yes | OrthoDB | NA | Add | G2F details (Cma2) DRscDB Data: (Cma2) |\n\n``` r\ndiopt(c('Eno2','Mog'),inTax = 10090, outTax =9606) %\u003e%\n knitr::kable()\n```\n\n| Input Order | Search Term | Mouse GeneID | MGIID | Mouse Symbol | Species 2 | Human GeneID | Human Species Gene ID | Human Symbol | Ensmbl ID (link HPA) | DIOPT Score | Weighted Score | Rank | Best Score | Best Score Reverse | Prediction Derived From | Alignment \u0026 Scores | Feedback | Gene Details |\n|--------------------------:|:------------|-------------:|------:|:-------------|:----------|-------------:|----------------------:|:-------------|:---------------------|------------:|---------------:|:---------|:-----------|:-------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------|:---------|:---------------------------------------|\n| 1 | Eno2 | 13807 | 95394 | Eno2 | Human | 2026 | 3353 | ENO2 | ENSG00000111674 | 14 | 14.29 | high | Yes | Yes | Compara, eggNOG, HGNC, Hieranoid, Homologene, Inparanoid, OMA, OrthoFinder, OrthoInspector, orthoMCL, Panther, Phylome, RoundUp, TreeFam | NA | Add | G2F details (ENO2) DRscDB Data: (ENO2) |\n| Human Protein Atlas (HPA) | | | | | | | | | | | | | | | | | | |\n| 1 | Eno2 | 13807 | 95394 | Eno2 | Human | 2023 | 3350 | ENO1 | ENSG00000074800 | 5 | 4.84 | moderate | No | No | eggNOG, OrthoDB, OrthoFinder, orthoMCL, RoundUp | NA | Add | G2F details (ENO1) DRscDB Data: (ENO1) |\n| Human Protein Atlas (HPA) | | | | | | | | | | | | | | | | | | |\n| 1 | Eno2 | 13807 | 95394 | Eno2 | Human | 2027 | 3354 | ENO3 | ENSG00000108515 | 4 | 3.83 | moderate | No | No | eggNOG, OrthoFinder, orthoMCL, RoundUp | NA | Add | G2F details (ENO3) DRscDB Data: (ENO3) |\n| Human Protein Atlas (HPA) | | | | | | | | | | | | | | | | | | |\n| 1 | Eno2 | 13807 | 95394 | Eno2 | Human | 2580 | 4113 | GAK | ENSG00000178950 | 1 | 1.01 | low | No | No | OrthoDB | NA | Add | G2F details (GAK) DRscDB Data: (GAK) |\n| Human Protein Atlas (HPA) | | | | | | | | | | | | | | | | | | |\n| 1 | Eno2 | 13807 | 95394 | Eno2 | Human | 2534 | 4037 | FYN | ENSG00000010810 | 1 | 1.01 | low | No | No | OrthoDB | NA | Add | G2F details (FYN) DRscDB Data: (FYN) |\n| Human Protein Atlas (HPA) | | | | | | | | | | | | | | | | | | |\n| 1 | Eno2 | 13807 | 95394 | Eno2 | Human | 387712 | 31670 | ENO4 | ENSG00000188316 | 1 | 0.90 | low | No | No | eggNOG | NA | Add | G2F details (ENO4) DRscDB Data: (ENO4) |\n| Human Protein Atlas (HPA) | | | | | | | | | | | | | | | | | | |\n| 2 | Mog | 17441 | 97435 | Mog | Human | 4340 | 7197 | MOG | ENSG00000204655 | 15 | 15.30 | high | Yes | Yes | Compara, eggNOG, HGNC, Hieranoid, Homologene, Inparanoid, OMA, OrthoDB, OrthoFinder, OrthoInspector, orthoMCL, Panther, Phylome, RoundUp, TreeFam | NA | Add | G2F details (MOG) DRscDB Data: (MOG) |\n| Human Protein Atlas (HPA) | | | | | | | | | | | | | | | | | | |\n\n# Mishaps\n\nAs of version version 1.1.68, the output now includes NCBI ids. Since it\ndoesn’t change any of the existing column names or their order, this\nshouldn’t cause problems in most use cases.\n\nIf a you can’t find a gene you are looking for it may have synonyms. See\n[geneSynonym](https://github.com/oganm/geneSynonym.git) package to find\nthem. If you have other problems open an issue or send a mail.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Foganm%2Fhomologene","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Foganm%2Fhomologene","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Foganm%2Fhomologene/lists"}