{ "_id": "69d62f9910581d1350dec99a", "Package": "biomartr", "Title": "Genomic Data Retrieval", "Version": "1.0.11", "Authors@R": "c(person(\"Hajk-Georg\", \"Drost\",\nrole = c(\"aut\", \"cre\"),\nemail = \"hajk-georg.drost@tuebingen.mpg.de\",\ncomment = c(ORCID = \"http://orcid.org/0000-0002-1567-306X\")),\nperson(\"Haakon\", \"Tjeldnes\",\nemail = \"hauken_heyken@hotmail.com\",\nrole = c(\"aut\", \"ctb\"))\n)", "Description": "Perform large scale genomic data retrieval and functional\nannotation retrieval. This package aims to provide users with a\nstandardized way to automate genome, proteome, 'RNA', coding\nsequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI\nRefSeq', 'NCBI Genbank', 'ENSEMBL', and 'UniProt' databases.\nFurthermore, an interface to the 'BioMart' database (Smedley et\nal. (2009) ) allows users to\nretrieve functional annotation for genomic loci. In addition,\nusers can download entire databases such as 'NCBI RefSeq'\n(Pruitt et al. (2007) ), 'NCBI nr',\n'NCBI nt', 'NCBI Genbank' (Benson et al. (2013)\n), etc. with only one command.", "VignetteBuilder": "knitr", "License": "GPL-2", "URL": "https://docs.ropensci.org/biomartr/,\nhttps://github.com/ropensci/biomartr", "BugReports": "https://github.com/ropensci/biomartr/issues", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibxml2-dev libssl-dev libx11-dev zlib1g-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2025-12-02 15:45:39 UTC", "RemoteUrl": "https://github.com/ropensci/biomartr", "RemoteRef": "master", "RemoteSha": "5affece1736b5d3198c788456320a262c63ceb8e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-04-08 09:09:21 UTC", "User": "root" }, "Author": "Hajk-Georg Drost [aut, cre] (ORCID:\n),\nHaakon Tjeldnes [aut, ctb]", "Maintainer": "Hajk-Georg Drost ", "MD5sum": "9a489ea4df38972f89b2a62dad3b9237", "_user": "ropensci", "_type": "src", "_file": "biomartr_1.0.11.tar.gz", "_fileid": 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directory to store back end files like kingdom summaries etc", "concept": [ "cachedir" ], "topics": [ "cachedir_set" ] }, { "page": "check_annotation_biomartr", "title": "Check whether an annotation file contains outlier lines", "topics": [ "check_annotation_biomartr" ] }, { "page": "clean.retrieval", "title": "Format 'meta.retrieval' output", "topics": [ "clean.retrieval" ] }, { "page": "download.database", "title": "Download a NCBI Database to Your Local Hard Drive", "topics": [ "download.database" ] }, { "page": "download.database.all", "title": "Download all elements of an NCBI databse", "topics": [ "download.database.all" ] }, { "page": "ensembl_divisions", "title": "List all available ENSEMBL divisions", "topics": [ "ensembl_divisions" ] }, { "page": "get.ensembl.info", "title": "Helper function to retrieve species information from the ENSEMBL API", "topics": [ "get.ensembl.info" ] }, { "page": "getAssemblyStats", "title": "Genome Assembly Stats Retrieval", "topics": [ 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"getGenome", "title": "Genome Retrieval", "concept": [ "genome", "getBio" ], "topics": [ "getGenome" ] }, { "page": "getGENOMEREPORT", "title": "Retrieve NCBI GENOME_REPORTS file", "topics": [ "getGENOMEREPORT" ] }, { "page": "getGenomeSet", "title": "Genome Retrieval of multiple species", "concept": [ "genome", "getBioSet" ], "topics": [ "getGenomeSet" ] }, { "page": "getGFF", "title": "Genome Annotation Retrieval (GFF3)", "concept": [ "getBio", "gff" ], "topics": [ "getGFF" ] }, { "page": "getGFFSet", "title": "GFF retrieval of multiple species", "concept": [ "getBioSet", "gff" ], "topics": [ "getGFFSet" ] }, { "page": "getGO", "title": "Gene Ontology Query", "topics": [ "getGO" ] }, { "page": "getGroups", "title": "Retrieve available groups for a kingdom of life (only available for NCBI RefSeq and NCBI Genbank)", "topics": [ "getGroups" ] }, { "page": "getGTF", "title": "Genome Annotation Retrieval (GTF)", "topics": [ "getGTF" ] }, { "page": "getKingdomAssemblySummary", "title": "Retrieve and summarise the assembly_summary.txt files from NCBI for all kingdoms", "topics": [ "getKingdomAssemblySummary" ] }, { "page": "getKingdoms", "title": "Retrieve available kingdoms of life", "topics": [ "getKingdoms" ] }, { "page": "getMarts", "title": "Retrieve information about available Ensembl Biomart databases", "concept": [ "biomaRt" ], "topics": [ "getMarts" ] }, { "page": "getMetaGenomeAnnotations", "title": "Retrieve annotation *.gff files for metagenomes from NCBI Genbank", "topics": [ "getMetaGenomeAnnotations" ] }, { "page": "getMetaGenomes", "title": "Retrieve metagenomes from NCBI Genbank", "topics": [ "getMetaGenomes" ] }, { "page": "getMetaGenomeSummary", "title": "Retrieve the assembly_summary.txt file from NCBI genbank metagenomes", "topics": [ "getMetaGenomeSummary" ] }, { "page": "getProteome", "title": "Proteome Retrieval", "concept": [ "getBio", "proteome" ], "topics": [ "getProteome" ] }, { "page": "getProteomeSet", "title": "Proteome retrieval of multiple species", "concept": [ "getBioSet", "proteome" ], "topics": [ "getProteomeSet" ] }, { "page": "getReleases", "title": "Retrieve available database releases or versions of ENSEMBL", "topics": [ "getReleases" ] }, { "page": "getRepeatMasker", "title": "Repeat Masker Retrieval", "topics": [ "getRepeatMasker" ] }, { "page": "getRNA", "title": "RNA Sequence Retrieval", "concept": [ "getBio", "rna" ], "topics": [ "getRNA" ] }, { "page": "getRNASet", "title": "RNA Retrieval of multiple species", "concept": [ "getBioSet", "rna" ], "topics": [ "getRNASet" ] }, { "page": "getSummaryFile", "title": "Helper function to retrieve the assembly_summary.txt file from NCBI", "topics": [ "getSummaryFile" ] }, { "page": "getUniProtInfo", "title": "Get uniprot info from organism", "topics": [ "getUniProtInfo" ] }, { "page": "getUniProtSTATS", "title": "Retrieve UniProt Database Information File (STATS)", "topics": [ "getUniProtSTATS" ] }, { "page": "is.genome.available", "title": "Check Genome 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