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biomartr
View on CRAN: Click
here
Download and install biomartr package within the R console
Install from CRAN:
install.packages("biomartr")
Install from Github:
library("remotes")
install_github("cran/biomartr")
Install by package version:
library("remotes")
install_version("biomartr", "1.0.7")
Attach the package and use:
library("biomartr")
Maintained by
Hajk-Georg Drost
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2015-07-22
Latest Update: 2023-06-20
Description:
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) ) allows users to retrieve
functional annotation for genomic loci. In addition, users can download entire databases such
as 'NCBI RefSeq' (Pruitt et al. (2007) ), 'NCBI nr',
'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) ), etc. with only one command.
How to cite:
Hajk-Georg Drost (2015). biomartr: Genomic Data Retrieval. R package version 1.0.7, https://cran.r-project.org/web/packages/biomartr
Previous versions and publish date:
0.0.1 (2015-07-22 16:15), 0.0.2 (2015-08-07 20:44), 0.0.3 (2016-03-02 17:18), 0.1.0 (2016-08-07 18:25), 0.2.0 (2016-11-22 09:07), 0.2.1 (2016-12-15 17:57), 0.3.0 (2017-02-09 19:59), 0.4.0 (2017-03-14 06:58), 0.5.1 (2017-05-28 21:08), 0.5.2 (2017-09-20 19:35), 0.7.0 (2018-01-03 02:06), 0.8.0 (2018-06-27 19:14), 0.9.0 (2019-05-21 19:40), 0.9.1 (2019-12-10 18:50), 0.9.2 (2020-01-11 00:00), 1.0.2 (2022-02-23 14:50), 1.0.3 (2023-05-07 23:40), 1.0.4 (2023-06-20 15:50), 1.0.5 (2023-10-04 17:50), 1.0.6 (2023-10-24 22:40)
Other packages that cited biomartr R package
View biomartr citation profile
Other R packages that biomartr depends,
imports, suggests or enhances
Functions, R codes and Examples using
the biomartr R package
Some associated functions: biomart . biomartr-package . cachedir . cachedir_set . check_annotation_biomartr . clean.retrieval . download.database.all . download.database . ensembl_divisions . get.ensembl.info . getAssemblyStats . getAttributes . getBio . getBioSet . getCDS . getCDSSet . getCollection . getCollectionSet . getDatasets . getENSEMBL.Seq . getENSEMBL.gtf . getENSEMBL . getENSEMBLGENOMESInfo . getENSEMBLInfo . getFilters . getGENOMEREPORT . getGFF . getGFFSet . getGO . getGTF . getGenome . getGenomeSet . getGroups . getKingdomAssemblySummary . getKingdoms . getMarts . getMetaGenomeAnnotations . getMetaGenomeSummary . getMetaGenomes . getProteome . getProteomeSet . getRNA . getRNASet . getReleases . getRepeatMasker . getSummaryFile . getUniProtInfo . getUniProtSTATS . is.genome.available . listDatabases . listGenomes . listGroups . listKingdoms . listMetaGenomes . meta.retrieval.all . meta.retrieval . organismAttributes . organismBM . organismFilters . read_assemblystats . read_cds . read_genome . read_gff . read_proteome . read_rm . read_rna . refseqOrganisms . summary_cds . summary_genome .
Some associated R codes: N50.R . Refseq_Genbank_ftp_generics.R . Refseq_Genbank_post_processing.R . biomart.R . biomartr-package.R . check_annotation_biomartr.R . clean.retrieval.R . clean_species_names_helper.R . connected.to.internet.R . custom_download.R . download_database.R . download_database_all.R . ensembl_ftp_generics.R . existingOrganisms.R . existingOrganisms_ensembl.R . exists.ftp.file.R . get.ensembl.info.R . get.ensemblgenome.info.R . getAssemblyStats.R . getAttributes.R . getBioSet.R . getCDS.R . getCDSSet.R . getCollection.R . getCollectionSet.R . getDatasets.R . getENSEMBL.Annotation.R . getENSEMBL.R . getENSEMBL.Seq.R . getENSEMBL.gtf.R . getENSEMBLGENOMES.Annotation.R . getENSEMBLGENOMES.R . getENSEMBLGENOMES.Seq.R . getENSEMBLGENOMES.gtf.R . getENSEMBLGENOMESInfo.R . getENSEMBLInfo.R . getFilters.R . getGENOMEREPORT.R . getGFF.R . getGFFSet.R . getGO.R . getGTF.R . getGenome.R . getGenomeSet.R . getGroups.R . getKingdomAssemblySummary.R . getKingdoms.R . getMarts.R . getMetaGenomeAnnotations.R . getMetaGenomeSummary.R . getMetaGenomes.R . getProteome.R . getProteomeSet.R . getRNA.R . getRNASet.R . getReleases.R . getRepeatMasker.R . getSet.R . getSubMarts.R . getSummaryFile.R . getUniProtInfo.R . getUniProtSTATS.R . getUniProtSeq.R . is.ensembl.alive.R . is.ensemblgenomes.alive.R . is.genome.available.R . is.taxid.R . listDatabases.R . listGenomes.R . listGroups.R . listKingdoms.R . listMetaGenomes.R . listNCBIDatabases.R . messages.R . meta.retrieval.R . meta.retrieval.all.R . organismAttributes.R . organismBM.R . organismFilters.R . readAssemblyDoc.R . read_assemblystats.R . read_cds.R . read_genome.R . read_gff.R . read_md5file.R . read_proteome.R . read_rm.R . read_rna.R . refseqOrganisms.R . summary_cds.R . summary_genome.R . test_url_status.R . tidy_name.R . tidy_name2.R . toupper_first_char.R . utils.R . Full biomartr package functions and examples
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