{"id":17606522,"url":"https://github.com/mhahsler/rblast","last_synced_at":"2025-05-16T19:03:19.298Z","repository":{"id":41848415,"uuid":"43840179","full_name":"mhahsler/rBLAST","owner":"mhahsler","description":"Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package","archived":false,"fork":false,"pushed_at":"2025-01-07T00:42:39.000Z","size":463,"stargazers_count":106,"open_issues_count":6,"forks_count":22,"subscribers_count":3,"default_branch":"devel","last_synced_at":"2025-04-03T20:10:28.010Z","etag":null,"topics":["bioconductor","bioinformatics","blast-search"],"latest_commit_sha":null,"homepage":"","language":"R","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/mhahsler.png","metadata":{"files":{"readme":"README.Rmd","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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2015-10-07T19:33:35.000Z","updated_at":"2025-04-03T12:40:06.000Z","dependencies_parsed_at":"2023-01-29T22:15:15.239Z","dependency_job_id":"aa7dd149-f649-4e69-83ed-6f020277c08e","html_url":"https://github.com/mhahsler/rBLAST","commit_stats":{"total_commits":39,"total_committers":4,"mean_commits":9.75,"dds":0.1282051282051282,"last_synced_commit":"413bf001e283b4d35038a7cc4493b6ad90613414"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mhahsler%2FrBLAST","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mhahsler%2FrBLAST/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mhahsler%2FrBLAST/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mhahsler%2FrBLAST/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mhahsler","download_url":"https://codeload.github.com/mhahsler/rBLAST/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248609545,"owners_count":21132915,"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","blast-search"],"created_at":"2024-10-22T15:44:44.654Z","updated_at":"2025-04-12T17:45:38.488Z","avatar_url":"https://github.com/mhahsler.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003cimg src=\"https://bioconductor.org/images/logo/svg/Logo.svg\" align=\"right\" /\u003e\n\n```{r echo=FALSE, results = 'asis'}\npkg \u003c- \"rBLAST\"\n\nsource(\"https://raw.githubusercontent.com/mhahsler/pkg_helpers/main/pkg_helpers.R\")\npkg_title(pkg, CRAN = FALSE, Bioc = TRUE)\n```\n\nInterfaces the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases with the Bioconductor infrastructure. This includes\ninterfaces to `blastn`, `blastp`, `blastx`, and `makeblastdb`.\nThe BLAST software needs to be downloaded and installed separately.\n\nOther R interfaces for bioinformatics are also available:\n\n* [rRDP](https://bioconductor.org/packages/rRDP): Interface to the RDP Classifier \n* [rMSA](https://mhahsler.r-universe.dev/rMSA): Interface for Popular Multiple \n    Sequence Alignment Tools including ClustalW, MAFFT, MUSCLE, and Kalign\n\n\n## Installation\n\n1. Install the BLAST software by following the instructions in the \n[INSTALL](https://github.com/mhahsler/rBLAST/blob/devel/INSTALL) file.\n\n2. Install the latest version of the R package\n    ```{r eval = FALSE}\n    if (!require(\"BiocManager\", quietly = TRUE)) {\n        install.packages(\"BiocManager\")\n    }\n    \n    # The following initializes usage of Bioc devel\n    BiocManager::install(version='devel')\n    \n    BiocManager::install(\"rBLAST\")\n    ```\n\n## Usage\n\n```{r, message=FALSE}\nlibrary(rBLAST)\n```\n\nDownload the prebuilt 16S Microbial data base from NCBI's ftp server at:\nhttps://ftp.ncbi.nlm.nih.gov/blast/db/\n\n```{r}\ntgz_file \u003c- blast_db_get(\"16S_ribosomal_RNA.tar.gz\")\nuntar(tgz_file, exdir = \"16S_rRNA_DB\")\n```\n\nLoad the downloaded BLAST database.\n```{r}\nbl \u003c- blast(db = \"./16S_rRNA_DB/16S_ribosomal_RNA\")\nbl\n```\n\nLoad some test sequences shipped with the package.\n\n```{r}\nseq \u003c- readRNAStringSet(system.file(\"examples/RNA_example.fasta\",\n    package = \"rBLAST\"\n))\nseq\n```\n\nQuery the BLAST database to find matches for the first test sequence\nwith a 99% percent identity or higher.\n\n```{r}\ncl \u003c- predict(bl, seq[1, ], BLAST_args = \"-perc_identity 99\")\ncl\n```\n\n```{r, include=FALSE}\nunlink(\"./16S_rRNA_DB\", recursive = TRUE)\n```\n\n## Citation Request\n\n```{r, echo=FALSE, results='asis', comment= \"\"}\npkg_citation(pkg)\n```\n\n## Acknowledgments\nThis work was partially supported by grant no. R21HG005912 from the [National Human Genome Research Institute](https://www.genome.gov/).\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmhahsler%2Frblast","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmhahsler%2Frblast","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmhahsler%2Frblast/lists"}