{"id":32111333,"url":"https://github.com/simeross/ggseqalign","last_synced_at":"2026-02-21T19:33:45.591Z","repository":{"id":241076005,"uuid":"803958774","full_name":"simeross/ggseqalign","owner":"simeross","description":"R package to plot pairwise alignments of strings, specifically DNA/AA sequences.","archived":false,"fork":false,"pushed_at":"2025-03-03T14:31:38.000Z","size":979,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-10-20T14:41:50.215Z","etag":null,"topics":["alignment","bioinformatics","ggplot2-enhancements","minimalistic","r","visualization"],"latest_commit_sha":null,"homepage":"","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/simeross.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","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,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-05-21T17:28:42.000Z","updated_at":"2025-03-03T14:31:43.000Z","dependencies_parsed_at":"2024-06-11T09:04:15.871Z","dependency_job_id":null,"html_url":"https://github.com/simeross/ggseqalign","commit_stats":null,"previous_names":["simeross/ggseqalign"],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/simeross/ggseqalign","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simeross%2Fggseqalign","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simeross%2Fggseqalign/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simeross%2Fggseqalign/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simeross%2Fggseqalign/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/simeross","download_url":"https://codeload.github.com/simeross/ggseqalign/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simeross%2Fggseqalign/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29691045,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-21T18:18:25.093Z","status":"ssl_error","status_checked_at":"2026-02-21T18:18:22.435Z","response_time":107,"last_error":"SSL_read: 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":["alignment","bioinformatics","ggplot2-enhancements","minimalistic","r","visualization"],"created_at":"2025-10-20T14:24:30.378Z","updated_at":"2026-02-21T19:33:45.585Z","avatar_url":"https://github.com/simeross.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cimg src=\"inst/hexlogo/hexlogo.png\" alt=\"ggseqalign hex sticker\" width=\"400\"/\u003e\n\n## Intro\nThis is an R package to perform pairwise alignments of strings and plot them in a minimal style that is suitable for strings/sequences of any length. It is compatible with ggplot2 and DNA/AA sequence objects from `Biostrings`.\n\n## Installation\n\n### Bioconductor\nI recommend installing `ggseqalign` from Bioconductor.\n```\nif (!require(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\nBiocManager::install(\"ggseqalign\")\n```\n\n### GitHub (R version 4.4.0 and above)\n`ggseqalign` can be installed from its original source on GitHub (requires `devtools`).\n```\ninstall.packages(\"devtools\")\ndevtools::install_git(\"https://github.com/simeross/ggseqalign.git\")\n```\n\n### earlier R versions\nIf you use any R version older than `4.4.0`, install version 0.1.0 of this package.\n```\ninstall.packages(\"devtools\")\ndevtools::install_git(\"https://github.com/simeross/ggseqalign@e1a2e99ee7d079d2e4331bc101382cfebe125fa8\")\n```\n\n## Quick start\nAll you need is this package and some strings to align and you are ready to go.\n```\nlibrary(ggseqalign)\n\nquery_strings \u003c- (c(\"boo\", \"fibububuzz\", \"bozz\", \"baofuzz\"))\nsubject_string \u003c- \"boofizz\"\n\nalignment \u003c- alignment_table(query_strings, subject_string)\n\nplot_sequence_alignment(alignment)\n```\n\u003cimg src=\"inst/figs/rm_ex1.png\" alt=\"output of the code above\" width=\"400\"/\u003e\n\n\nTo align DNA or AA sequences from a fasta file, read them in with `Biostrings`\n```\nlibrary(ggseqalign)\nlibrary(Biostrings)\n\nquery_sequences \u003c- Biostrings::readDNAStringSet(\"my_multi_sequence_fasta.fa\")\nsubject_sequence \u003c- Biostrings::readDNAStringSet(\"my_reference_fasta.fa\")\n\nalignment \u003c- alignment_table(query_sequences, subject_sequence)\n\npl \u003c- plot_sequence_alignment(alignment)\npl\n```\n\u003cimg src=\"inst/figs/rm_ex2.png\" alt=\"output of the code above\" width=\"400\"/\u003e\n\n\nTo style the plot generated above to your own taste, use `ggplot2`, for example:\n```\nlibrary(ggplot2)\n \npl +\n ylab(\"Sequence variants\") +\n xlab(\"Length in bp\") +\n scale_color_viridis_d() +\n theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1),\n    axis.title = element_text())\n```\n\u003cimg src=\"inst/figs/rm_ex3.png\" alt=\"output of the code above\" width=\"400\"/\u003e\n\n\n### Bug reports\nIf you come across bugs, please [submit an issue](https://github.com/simeross/ggseqalign/issues)\n\n### License\nArtistic License 2.0.\n\n### Credit\nThe research and data generation that was a major motivation for me to finally create this package has received funding from the Norwegian Financial Mechanism 2014-2021, [project DivGene: UMO-2019/34/H/NZ9/00559](https://eeagrants.org/archive/2014-2021/projects/PL-Basic%20Research-0012)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsimeross%2Fggseqalign","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsimeross%2Fggseqalign","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsimeross%2Fggseqalign/lists"}