{"id":18189940,"url":"https://github.com/kullrich/korthor","last_synced_at":"2026-02-07T12:32:10.802Z","repository":{"id":225502693,"uuid":"765751939","full_name":"kullrich/korthoR","owner":"kullrich","description":"korthoR calculates pairwise kmer jaccard distance between all sequences of an AAStringSet ","archived":false,"fork":false,"pushed_at":"2024-03-05T07:04:23.000Z","size":816,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-07-30T15:30:58.262Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/kullrich.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-03-01T14:48:39.000Z","updated_at":"2024-11-04T17:00:39.000Z","dependencies_parsed_at":"2024-12-21T04:29:12.743Z","dependency_job_id":"a8033bea-6a8c-43fc-96fb-39fd2e22cd97","html_url":"https://github.com/kullrich/korthoR","commit_stats":{"total_commits":7,"total_committers":1,"mean_commits":7.0,"dds":0.0,"last_synced_commit":"4c41376d762ac10f1bd04890901b739f0965b774"},"previous_names":["kullrich/korthor"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/kullrich/korthoR","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2FkorthoR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2FkorthoR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2FkorthoR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2FkorthoR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kullrich","download_url":"https://codeload.github.com/kullrich/korthoR/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2FkorthoR/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29194019,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-07T07:37:03.739Z","status":"ssl_error","status_checked_at":"2026-02-07T07:37:03.029Z","response_time":63,"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":[],"created_at":"2024-11-03T04:04:38.031Z","updated_at":"2026-02-07T12:32:10.787Z","avatar_url":"https://github.com/kullrich.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# korthoR \u003ca href=\"https://github.com/kullrich/korthoR\"\u003e\u003cimg src=\"man/figures/logo.png\" align=\"right\" height=\"160\" /\u003e\u003c/a\u003e\n\n`korthoR` calculates pairwise kmer jaccard distance between all sequences of an `AAStringSet`.\n\n## Installation instructions\n\n## R specific installation prerequisites\n\n### install packages from [cran](https://cran.r-project.org/web/packages/index.html)\n\nIn most cases you need to first install the following system-wide packages to be able to compile the R dependencies. If you do not have 'sudo' rights, please ask your system-admin to install them for you.\n\nUbuntu/Debian\n\n```\nsudo apt-get install libcurl4-openssl-dev libssl-dev libxml2-dev libglu1-mesa-dev libgit2-dev\n#Pandoc is required to build R Markdown vignettes\n#sudo apt-get install pandoc\n#pkgdown dependencies - pkgdown is used to build R package pages\n#sudo apt-get install libssh2-1-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev\n```\n\nCentOS\n\n```\nsudo yum install libcurl-devel openssl-devel libxml2-devel mesa-libGLU-devel libgit2-devel\n#Pandoc is required to build R Markdown vignettes\n#sudo yum install pandoc\n#pkgdown dependencies - pkgdown is used to build R package pages\n#sudo yum install libssh2-devel fontconfig-devel harfbuzz-devel fribidi-devel freetype-devel libpng-devel libtiff-devel libjpeg-turbo-devel\n```\n\n- [Rcpp](https://cran.r-project.org/web/packages/Rcpp/index.html)\n- [RcppThread](https://cran.r-project.org/web/packages/RcppThread/index.html)\n- [devtools](https://cran.r-project.org/web/packages/devtools/index.html)\n- [testthat](https://cran.r-project.org/web/packages/testthat/index.html)\n- [reshape2](https://cran.r-project.org/web/packages/reshape2/index.html)\n- [dplyr](https://cran.r-project.org/web/packages/dplyr/index.html)\n- [ape](https://cran.r-project.org/web/packages/ape/index.html)\n\n```\ninstall.packages(\"Rcpp\")\ninstall.packages(\"RcppThread\")\ninstall.packages(\"devtools\")\ninstall.packages(\"testthat\")\ninstall.packages(\"reshape2\")\ninstall.packages(\"dplyr\")\ninstall.packages(\"ape\")\n```\n\n### install packages from [Bioconductor](https://www.bioconductor.org/)\n\n- [MSA2dist](https://bioconductor.org/packages/release/bioc/html/MSA2dist.html)\n\n```\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\nBiocManager::install(\n    c(\n    \"MSA2dist\")\n)\n```\n\n### install [korthoR](https://github.com/kullrich/korthoR)\n\n```\ndevtools::install_github(\"kullrich/korthoR\", build_vignettes = TRUE, dependencies = TRUE)\n```\n\n## Quick-guide\n\n```\nlibrary(korthoR)\n\n## load example sequence data\ndata(\"hiv\", package=\"MSA2dist\")\n\n## count kmers of length 6 for all amino acids\nl \u003c- hiv |\u003e\n    MSA2dist::cds2aa() |\u003e\n    korthoR::count_kmers(k=6)\nl\n\n## count kmers using multiple threads\nl \u003c- hiv |\u003e\n    MSA2dist::cds2aa() |\u003e\n    korthoR::count_kmers(k=6, threads=2)\nl\n\n## get jaccard distance\nhiv |\u003e\n    MSA2dist::cds2aa() |\u003e\n    korthoR::count_kmers(k=6) |\u003e\n    korthoR::get_jaccard_from_self(k=6)\n\n## get jaccard distance using multiple threads\nhiv |\u003e\n    MSA2dist::cds2aa() |\u003e\n    korthoR::count_kmers(k=6, threads=2) |\u003e\n    korthoR::get_jaccard_from_self(k=6, threads=2)\n\n## get bionjs tree\ndata(hiv, package=\"MSA2dist\")\nl \u003c- hiv |\u003e\n    MSA2dist::cds2aa() |\u003e\n    korthoR::count_kmers(k=6)\nd \u003c- korthoR::get_jaccard_a_b(kmer_counts_q=l,\n    kmer_counts_t=l,\n    k=6)\nt1 \u003c- get_bionjs_tree(jaccard_df=d, value=\"jaccard\")\nt2 \u003c- get_bionjs_tree(jaccard_df=d, value=\"mash\")\nt3 \u003c- get_bionjs_tree(jaccard_df=d, value=\"sumdist\")\npar(mfrow=c(1,3))\nplot(t1, main=\"jaccard\")\nplot(t2, main=\"mash\")\nplot(t3, main=\"sumdist\")\n```\n\n\u003cimg src=\"./man/figures/bionjs_trees.png\" alt=\"Figure: bionjs trees from the `get_bionjs_tree()` function\" width=\"640\"\u003e\n\n## License\n\nGPL-3 (see LICENSE)\n\n## Contributing Code\n\nIf you would like to contribute to korthoR, please file an issue so that one can establish a statement of need, avoid redundant work, and track progress on your contribution.\n\nBefore you do a pull request, you should always file an issue and make sure that someone from the korthoR developer team agrees that it's a problem, and is happy with your basic proposal for fixing it.\n\nOnce an issue has been filed and we've identified how to best orient your contribution with package development as a whole, [fork](https://docs.github.com/en/github/getting-started-with-github/fork-a-repo) the [main repo](https://github.com/kullrich/korthoR.git), branch off a [feature branch](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/about-branches) from `main`, [commit](https://docs.github.com/en/desktop/contributing-and-collaborating-using-github-desktop/committing-and-reviewing-changes-to-your-project) and [push](https://docs.github.com/en/github/using-git/pushing-commits-to-a-remote-repository) your changes to your fork and submit a [pull request](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/proposing-changes-to-your-work-with-pull-requests) for `korthoR:main`.\n\nBy contributing to this project, you agree to abide by the Code of Conduct terms.\n\n## Bug reports\n\nPlease report any errors or requests regarding [korthoR](https://github.com/kullrich/korthoR) to Kristian Ullrich (ullrich@evolbio.mpg.de)\n\nor use the issue tracker at [https://github.com/kullrich/korthoR/issues](https://github.com/kullrich/korthoR/issues)\n\n## Code of Conduct - Participation guidelines\n\nThis repository adhere to [Contributor Covenant](https://contributor-covenant.org) code of conduct for in any interactions you have within this project. (see [Code of Conduct](https://github.com/kullrich/korthoR/-/blob/main/CODE_OF_CONDUCT.md))\n\nSee also the policy against sexualized discrimination, harassment and violence for the Max Planck Society [Code-of-Conduct](https://www.mpg.de/11961177/code-of-conduct-en.pdf).\n\nBy contributing to this project, you agree to abide by its terms.\n\n## References\n\nPagès H., Aboyoun P., Gentleman R., and DebRoy S. (2017). **Biostrings: Efficient manipulation of biological strings.** *R package version*, 2.56.0. [Biostrings](http://bioconductor.org/packages/release/bioc/html/Biostrings.html)\n\nParadis E., Schliep K. (2019). **ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R.** *Bioinformatics*, **35**, 526-528.[https://doi.org/10.1093/bioinformatics/bty633](https://doi.org/10.1093/bioinformatics/bty633)\n\nScrucca L., Fraley C., Murphy T.B., Raftery A.E.(2023). **Model-based clustering, classification, and density estimation using mclust in R.** *Chapman and Hall/CRC* [https://doi.org/10.1201/9781003277965](https://doi.org/10.1201/9781003277965)\n\nSheikhizadeh A.S., de Ridder D., Schranz M.E., Smit S. (2018). **Efficient inference of homologs in large eukaryotic pan-proteomes.** *BMC bioinformatics*,*. 2018 Dec; **19(1)**, 1-1. [https://doi.org/10.1186/s12859-018-2362-4](https://doi.org/10.1186/s12859-018-2362-4)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkullrich%2Fkorthor","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkullrich%2Fkorthor","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkullrich%2Fkorthor/lists"}