{"id":19837297,"url":"https://github.com/nvelden/geneviewer","last_synced_at":"2025-05-01T18:30:41.028Z","repository":{"id":213591743,"uuid":"667194362","full_name":"nvelden/geneviewer","owner":"nvelden","description":"An R package designed for drawing gene arrow maps","archived":false,"fork":false,"pushed_at":"2025-04-23T18:46:00.000Z","size":12068,"stargazers_count":76,"open_issues_count":3,"forks_count":4,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-04-23T19:47:07.068Z","etag":null,"topics":["genetics","r"],"latest_commit_sha":null,"homepage":"https://nvelden.github.io/geneviewer/","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/nvelden.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2023-07-17T00:20:22.000Z","updated_at":"2025-04-23T18:46:03.000Z","dependencies_parsed_at":"2024-01-18T04:56:18.393Z","dependency_job_id":"a2e2e43a-b55c-45be-9fef-4c69ad34e08c","html_url":"https://github.com/nvelden/geneviewer","commit_stats":null,"previous_names":["nvelden/gcviewer","nvelden/geneviewer"],"tags_count":10,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nvelden%2Fgeneviewer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nvelden%2Fgeneviewer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nvelden%2Fgeneviewer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nvelden%2Fgeneviewer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nvelden","download_url":"https://codeload.github.com/nvelden/geneviewer/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250505682,"owners_count":21441721,"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":["genetics","r"],"created_at":"2024-11-12T12:14:01.972Z","updated_at":"2025-05-01T18:30:36.020Z","avatar_url":"https://github.com/nvelden.png","language":"R","funding_links":[],"categories":["Visualization"],"sub_categories":["Biological Data"],"readme":"\u003cp align=\"center\"\u003e\n  \u003cimg src=\"man/figures/logo.png\" class=\"pkgdown-hide\" height=\"150px\" align=\"right\"\u003e\n  \u003ch1\u003e\u003cstrong\u003egeneviewer\u003c/strong\u003e - Gene Cluster Visualizations in R\u003c/h1\u003e\n\u003c/p\u003e\n\n\u003c!-- badges: start --\u003e\n\n[![R-CMD-check](https://github.com/nvelden/geneviewer/workflows/R-CMD-check/badge.svg)](https://github.com/nvelden/geneviewer/actions) [![CRAN status](https://www.r-pkg.org/badges/version/geneviewer)](https://CRAN.R-project.org/package=geneviewer) ![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)\n\n\u003c!-- badges: end --\u003e\n\n## geneviewer\n\n**geneviewer** is an R package for plotting gene clusters and transcripts. It imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. The package offers extensive customization options, including legends, labels, annotations, scales, colors, tooltips, and more. To explore all features visit the [package website](https://nvelden.github.io/geneviewer/articles/geneviewer.html).\n\n## Installation\n\n**geneviewer** is still in the development stage which might lead to breaking changes and thus not yet released on CRAN. You can install the development version from [GitHub](https://github.com/) with:\n\n``` r\n# install.packages(\"devtools\")\ndevtools::install_github(\"nvelden/geneviewer\")\n```\n\n## Usage\n\nThe below example demonstrates using **geneviewer** to plot a gene cluster on a genomic sequence, using the start and end positions of each gene. The genes are grouped by class and labels are added using the `GC_labels` function.\n\n``` r\nlibrary(geneviewer)\n\n# Data\ngene_cluster \u003c- data.frame(\n  name = c(\"ophB1\", \"ophC\", \"ophA\", \"ophD\", \"ophB2\", \"ophP\", \"ophE\"),\n  start = c(2522, 5286, 9536, 12616, 13183, 19346, 20170),\n  end = c(4276, 4718, 10904, 11859, 15046, 16016, 21484),\n  class = c(\"Monooxygenase\", \"NTF2-like\", \"Methyltransferase\", \n  \"O-acyltransferase\", \"Monooxygenase\", \"Prolyloligopeptidase\", \n  \"F-box/RNHI-like\")\n)\n\n# Chart\nGC_chart(gene_cluster, group = \"class\", height = \"100px\") %\u003e%\n  GC_labels(\"name\")\n```\n\n\u003cimg src=\"man/figures/ophA_gene_cluster.png\"/\u003e\n\n## Examples\n\nFor additional examples and the corresponding code to create the plots, please visit the [Examples](https://nvelden.github.io/geneviewer/articles/Examples.html) section.\n\n\u003cimg src=\"man/figures/erythromycin_BlastP.png\"/\u003e\n\n\u003chr\u003e\n\n\u003cimg src=\"man/figures/BRCA1_splice_variants.png\"/\u003e\n\n\u003chr\u003e\n\n\u003cimg src=\"man/figures/MUMmer.png\"/\u003e\n\n\u003chr\u003e\n\n\u003cimg src=\"man/figures/erythromycin_link.png\"/\u003e\n\n\u003chr\u003e\n\n\u003cimg src=\"man/figures/ophA_clusters.png\"/\u003e\n\n\u003chr\u003e\n\n\u003cimg src=\"man/figures/ophA_gene_links.png\"/\u003e\n\n\u003chr\u003e\n\n\u003cimg src=\"man/figures/erythromycin_cluster.png\"/\u003e\n\n\u003chr\u003e\n\n\u003cimg src=\"man/figures/human_hox_genes.png\"/\u003e\n\n## Issues\n\nIf you encounter any issues or have feature requests, please open an [Issue](https://github.com/nvelden/geneviewer/issues).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnvelden%2Fgeneviewer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnvelden%2Fgeneviewer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnvelden%2Fgeneviewer/lists"}