{"id":13720141,"url":"https://github.com/bernatgel/karyoploteR","last_synced_at":"2025-05-07T12:30:51.925Z","repository":{"id":43165369,"uuid":"60629250","full_name":"bernatgel/karyoploteR","owner":"bernatgel","description":"karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome","archived":false,"fork":false,"pushed_at":"2024-01-11T12:51:15.000Z","size":3212,"stargazers_count":296,"open_issues_count":59,"forks_count":42,"subscribers_count":7,"default_branch":"devel","last_synced_at":"2024-09-20T07:35:28.567Z","etag":null,"topics":["bioconductor","bioinformatics","data-visualization","genome","genomics-visualization","plotting-in-r","rstats"],"latest_commit_sha":null,"homepage":"https://bernatgel.github.io/karyoploter_tutorial/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bernatgel.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null}},"created_at":"2016-06-07T16:32:27.000Z","updated_at":"2024-09-11T17:42:55.000Z","dependencies_parsed_at":"2023-11-18T00:13:20.506Z","dependency_job_id":"14161e76-2623-4d87-8248-6337ef9e53ee","html_url":"https://github.com/bernatgel/karyoploteR","commit_stats":{"total_commits":550,"total_committers":12,"mean_commits":"45.833333333333336","dds":0.2909090909090909,"last_synced_commit":"6b61c4df4b7e1aa62e474405f8c2b9ee93ee36db"},"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bernatgel%2FkaryoploteR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bernatgel%2FkaryoploteR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bernatgel%2FkaryoploteR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bernatgel%2FkaryoploteR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bernatgel","download_url":"https://codeload.github.com/bernatgel/karyoploteR/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224597065,"owners_count":17337838,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":["bioconductor","bioinformatics","data-visualization","genome","genomics-visualization","plotting-in-r","rstats"],"created_at":"2024-08-03T01:01:00.229Z","updated_at":"2024-11-14T09:30:51.967Z","avatar_url":"https://github.com/bernatgel.png","language":"R","funding_links":[],"categories":["Ideogram"],"sub_categories":[],"readme":"[![Build Status](https://travis-ci.org/bernatgel/karyoploteR.svg?branch=master)](https://travis-ci.org/bernatgel/karyoploteR)\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)\n\n# karyoploteR - An R/Biocondutor package to plot arbitrary data along the genome\n\n\n![karyoploteR Example](https://raw.githubusercontent.com/bernatgel/karyoploter_tutorial/master/docs/Examples/MultipleDataTypes/images/Figure-1.png\n \"Example of plot created with karyoploteR\")\n\n## Description\n\n[karyoploteR](http://bioconductor.org/packages/karyoploteR) is an R package to \nplot data along the genome using a karyotype style plot.\n\nIt is entirely based on R base graphics and inspired by the R base graphics API. \nIt includes functions to plot primitive graphic elements such as points, lines,\nrectangles, text, etc mapped into the genome plot coordinates and higher \nlevel functions to plot a heatmap, the regions in a GenomicRanges object\nor the cumulative coverage of such regions.\n\nData positioning and track configuration has been inspired by Circos and does\nnot explicitly understands the concept of track. Thus, it is possible to freely specify \nwhere to plot the data and to create plots with multiple independent tracks or\noverlapping representations.\n\nIt is highly configurable and in addition to the parametrization of the \ndifferent data plotting functions, it is possible to specify custom functions \nfor every plotting action from the basic chromosome bands to the chromosome labels\nor base numbers as well as creating completely new plotting functions.\n\n## How to use it\n\nDocumentation ([vignette](http://bioconductor.org/packages/devel/bioc/vignettes/karyoploteR/inst/doc/karyoploteR.pdf) and [user manual](http://bioconductor.org/packages/devel/bioc/manuals/karyoploteR/man/karyoploteR.pdf)) is available at the karyoploteR's \nBioconductor landing page at [http://bioconductor.org/packages/karyoploteR](http://bioconductor.org/packages/karyoploteR)\n\n## Tutorial and Examples\n\nIn addition to the documentation above, a short tutorial and some examples can be found at [https://bernatgel.github.io/karyoploter_tutorial/](https://bernatgel.github.io/karyoploter_tutorial/)\n\n## \u003ca name=\"Citing\"\u003e\u003c/a\u003eCiting karyoploteR\n\nkaryoploteR has been developed by [Bernat Gel](https://twitter.com/bernatgel) and [Eduard Serra](mailto:eserra@igtp.cat) at [IGTP](http://www.germanstrias.org/)\nHereditary Cancer Group.\n\nIf you use karyoploteR in your research, please cite the [Bioinformatics paper](https://academic.oup.com/bioinformatics/article/3857734/karyoploteR-an-R-Bioconductor-package-to-plot) describing it:\n\nBernat Gel \u0026 Eduard Serra. (2017). *karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data*. Bioinformatics, 31–33. [doi:10.1093/bioinformatics/btx346](https://doi.org/10.1093/bioinformatics/btx346)\n\n## A few example plots created with karyoploteR\n\nThese images are all created with karyoploteR and are part of the documented \nexamples in the [karyoploteR's tutorial and examples page](https://bernatgel.github.io/karyoploter_tutorial/).\nClick on them to see how the code needed to create them.\n\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://bernatgel.github.io/karyoploter_tutorial/Examples/GeneExpression/GeneExpression.html\" target=\"_blank\"\u003e\n    \u003cimg src=\"https://bernatgel.github.io/karyoploter_tutorial/Examples/GeneExpression/images/Figure13-1.png\" width=\"40%\"  alt=\"A karyoploteR example plotting differential expression results computed with RNA-seq data from Drosophila Melanogaster\" title=\"Differential expression results computed with RNA-seq data from Drosophila Melanogaster\" style=\"max-width:100%;margin-right:5%;\" \u003e\u003c/img\u003e\n  \u003c/a\u003e\n  \u003ca href=\"https://bernatgel.github.io/karyoploter_tutorial//Examples/GeneDensityIdeograms/GeneDensityIdeograms.html\" target=\"_blank\"\u003e\n    \u003cimg src=\"https://bernatgel.github.io/karyoploter_tutorial//Examples/GeneDensityIdeograms/images/Figure9-1.png\" width=\"40%\"  alt=\"A karyoploteR example plotting the density of genes instead of the ideograms\" title=\"Usiong the density of genes instead of ideograms\"\u003e\u003c/img\u003e \n  \u003c/a\u003e\n  \u003cbr\u003e\n  \u003cbr\u003e\n  \u003ca href=\"https://bernatgel.github.io/karyoploter_tutorial//Examples/NucleotideFrequency/NucleotideFrequency.html\" target=\"_blank\"\u003e\n    \u003cimg src=\"https://bernatgel.github.io/karyoploter_tutorial//Examples/NucleotideFrequency/images/Figure11-1.png\" width=\"40%\"  alt=\"A karyoploteR example plotting the nucleotide frequency, genes and CpG-islands on a small genomic region\" title=\"The nucleotide frequency, genes and CpG-islands on a small genomic region\"\u003e\u003c/img\u003e\n  \u003c/a\u003e\n  \u003ca href=\"https://bernatgel.github.io/karyoploter_tutorial//Examples/SNPArray/SNPArray.html\" target=\"_blank\"\u003e\n    \u003cimg src=\"https://bernatgel.github.io/karyoploter_tutorial//Examples/SNPArray/images/Figure4-1.png\" width=\"40%\"  alt=\"A karyoploteR example plotting raw SNP-array data\" title=\"Raw SNP-array data\"\u003e\u003c/img\u003e\n  \u003c/a\u003e\n  \u003cbr\u003e\n  \u003cbr\u003e\n  \u003ca href=\"https://bernatgel.github.io/karyoploter_tutorial//Examples/PVivaxGenes/PVivaxGenes.html\" target=\"_blank\"\u003e\n    \u003cimg src=\"https://bernatgel.github.io/karyoploter_tutorial//Examples/PVivaxGenes/images/Figure6-1.png\" width=\"40%\"  alt=\"A karyoploteR example plotting the genes from Plasmodium Vivax PvP01 genome version\" title=\"The genes from Plasmodium Vivax PvP01 genome version\"\u003e\u003c/img\u003e\n  \u003c/a\u003e\n  \u003ca href=\"https://bernatgel.github.io/karyoploter_tutorial//Examples/PlotGenes/PlotGenes.html\" target=\"_blank\"\u003e\n    \u003cimg src=\"https://bernatgel.github.io/karyoploter_tutorial//Examples/PlotGenes/images/Figure2-1.png\" width=\"40%\"  alt=\"A karyoploteR example plotting genes positioned on the genome\" title=\"Genes positioned on the genome\"\u003e\u003c/img\u003e\n  \u003c/a\u003e\n  \u003cbr\u003e\n  \u003cbr\u003e\n  \u003ca href=\"https://bernatgel.github.io/karyoploter_tutorial//Examples/Rainfall/Rainfall.html\" target=\"_blank\"\u003e\n    \u003cimg src=\"https://bernatgel.github.io/karyoploter_tutorial//Examples/Rainfall/images/Figure3-1.png\" width=\"40%\"  alt=\"A karyoploteR example plotting a rainfall plot showing the distances between consecutive somatic variants\" title=\"A rainfall plot showing the distances between consecutive somatic variants\"\u003e\u003c/img\u003e\n  \u003c/a\u003e  \n  \u003ca href=\"https://bernatgel.github.io/karyoploter_tutorial//Examples/CpGIslands/CpGIslands.html\" target=\"_blank\"\u003e\n    \u003cimg src=\"https://bernatgel.github.io/karyoploter_tutorial//Examples/CpGIslands/images/Figure5-1.png\" width=\"40%\"  alt=\"A karyoploteR example plotting the density and positions of CpG islands along the genome\" title=\"The density and positions of CpG islands along the genome\"\u003e\u003c/img\u003e\n  \u003c/a\u003e\n\u003c/p\u003e\n\n\n\n\n\n\n\n\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbernatgel%2FkaryoploteR","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbernatgel%2FkaryoploteR","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbernatgel%2FkaryoploteR/lists"}