Other packages > Find by keyword >

biomartr  

Genomic Data Retrieval
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]
All associated links for this package
First Published: 2015-07-22
Latest Update: 2023-12-02
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. Accessed 10 Nov. 2026.
Previous versions and publish date:
(2026-07-09 07:22), 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
Complete documentation for biomartr
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
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

OBIC  
Calculate the Open Bodem Index (OBI) Score
The Open Bodem Index (OBI) is a method to evaluate the quality of soils of agricultural fields in Th ...
Download / Learn more Package Citations See dependency  
MazamaSpatialUtils  
Spatial Data Download and Utility Functions
A suite of conversion functions to create internally standardized spatial polygons data frames. Uti ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
CNLTtsa  
Complex-Valued Wavelet Lifting for Univariate and Bivariate Time Series Analysis
Implementations of recent complex-valued wavelet spectral procedures for analysis of irregularly sam ...
Download / Learn more Package Citations See dependency  
cosinor2  
Extended Tools for Cosinor Analysis of Rhythms
Statistical procedures for calculating population ...
Download / Learn more Package Citations See dependency  
rbooster  
AdaBoost Framework for Any Classifier
This is a simple package which provides a function that boosts pre-ready or custom-made classifiers ...
Download / Learn more Package Citations See dependency  

29,369

R Packages

247,686

Dependencies

77,665

Author Associations

29,370

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA