Package: biomartr 1.0.10
biomartr: Genomic Data Retrieval
Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL', and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. In addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. with only one command.
Authors:
biomartr_1.0.10.tar.gz
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biomartr_1.0.10.tgz(r-4.5-any)biomartr_1.0.10.tgz(r-4.4-any)biomartr_1.0.10.tgz(r-4.3-any)
biomartr_1.0.10.tar.gz(r-4.5-noble)biomartr_1.0.10.tar.gz(r-4.4-noble)
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biomartr.pdf |biomartr.html✨
biomartr/json (API)
NEWS
# Install 'biomartr' in R: |
install.packages('biomartr', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org')) |
Reviews:rOpenSci Software Review #93
Bug tracker:https://github.com/ropensci/biomartr/issues
Pkgdown site:https://docs.ropensci.org
biomartgenomic-data-retrievalannotation-retrievaldatabase-retrievalncbiensemblbiological-data-retrievalensembl-serversgenomegenome-annotationgenome-retrievalgenomicsmeta-analysismetagenomicsncbi-genbankpeer-reviewedproteomesequenced-genomes
Last updated 1 months agofrom:21aa0a2e0c (on master). Checks:1 OK, 7 WARNING. Indexed: yes.
Target | Result | Latest binary |
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Doc / Vignettes | OK | Feb 12 2025 |
R-4.5-win | WARNING | Feb 19 2025 |
R-4.5-mac | WARNING | Feb 12 2025 |
R-4.5-linux | WARNING | Feb 12 2025 |
R-4.4-win | WARNING | Feb 12 2025 |
R-4.4-mac | WARNING | Feb 12 2025 |
R-4.3-win | WARNING | Feb 12 2025 |
R-4.3-mac | WARNING | Feb 12 2025 |
Exports:biomartcachedircachedir_setcheck_annotation_biomartrdownload.databasedownload.database.allensembl_divisionsget.ensembl.infogetAssemblyStatsgetAttributesgetBioSetgetCDSgetCDSSetgetCollectiongetCollectionSetgetDatasetsgetENSEMBLGENOMESInfogetENSEMBLInfogetFiltersgetGenomegetGENOMEREPORTgetGenomeSetgetGFFgetGFFSetgetGOgetGroupsgetGTFgetKingdomAssemblySummarygetKingdomsgetMartsgetMetaGenomeAnnotationsgetMetaGenomesgetMetaGenomeSummarygetProteomegetProteomeSetgetReleasesgetRepeatMaskergetRNAgetRNASetgetSummaryFilegetUniProtInfogetUniProtSTATSis.genome.availablelistDatabaseslistGenomeslistGroupslistKingdomslistMetaGenomeslistNCBIDatabasesmeta.retrievalmeta.retrieval.allorganismAttributesorganismBMorganismFiltersread_assemblystatsread_cdsread_genomeread_gffread_proteomeread_rmread_rnarefseqOrganismssummary_cdssummary_genome
Dependencies:AnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64bitopsblobcachemclicliprcpp11crayoncurldata.tableDBIdbplyrdigestdownloaderdplyrfansifastmapfilelockfsgenericsGenomeInfoDbGenomeInfoDbDatagluehmshttrhttr2IRangesjsonliteKEGGRESTKernSmoothlifecyclemagrittrmemoisemimeopensslphilentropypillarpkgconfigplogrpngpoormanprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsRcppRCurlreadrrlangRSQLiteS4VectorsstringistringrsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsvroomwithrXMLxml2XVector
Ensembl BioMart Examples
Rendered fromBioMart_Examples.Rmd
usingknitr::rmarkdown
on Feb 12 2025.Last update: 2023-08-17
Started: 2017-03-13
Functional Annotation with biomartr
Rendered fromFunctional_Annotation.Rmd
usingknitr::rmarkdown
on Feb 12 2025.Last update: 2023-08-17
Started: 2014-11-27
Meta-Genome Retrieval
Rendered fromMetaGenome_Retrieval.Rmd
usingknitr::rmarkdown
on Feb 12 2025.Last update: 2024-12-12
Started: 2016-10-11
NCBI Database Retrieval
Rendered fromDatabase_Retrieval.Rmd
usingknitr::rmarkdown
on Feb 12 2025.Last update: 2022-02-22
Started: 2015-11-08
Sequence Retrieval
Rendered fromSequence_Retrieval.Rmd
usingknitr::rmarkdown
on Feb 12 2025.Last update: 2024-12-12
Started: 2014-11-27