biomartr

1.0.7

Genomic Data Retrieval

0packages depend

20.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Hajk-Georg DrostFirst published 2015-07-2221 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("biomartr", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ropensci/biomartr")

Development version from ropensci/biomartr. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-biomartr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

Slowest check: 6.3 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.22

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-07
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 8 earlier snapshots

ERROR2026-06-05
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-01
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-23
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-21
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-25
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-22
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,786 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 10%
Documented parameters: 98%
Return-value docs: 52%
References docs: 4%

Downloads

20.3K

CRAN downloads in the past year

Rank #3,395 · ~56/day · ~1.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.2K30 days

3.4K90 days

20.3K1 year

Compare downloads with other packages →

Also on541 r2u1.9K bioconda16 c2d4u

Repository

GitHub ↗ ropensci/biomartr

225Stars

28Forks

8Open issues

0Open PRs

12Releases

2,447Commits

11Contributors

rgenome-retrievalbiomartdatabase-retrievalncbi-genbankgenomicsensembl-serverssequenced-genomes

2,447 commits · Last activity 2025-12-02 · 0% stars, 30d

Stars over time

2025-05-17 · 2202026-07-07 · 225

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/ropensci/biomartr on 2026-07-30.

Continuous integration (1)

Travis CI

Research and citation (1)

codemeta.json

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.1

Imports (18)

biomaRt Biostrings curl tibble jsonlite data.table (>= 1.9.4)dplyr readr downloader (>= 0.3)RCurl XML httr stringr purrr R.utils philentropy withr fs

LinkingTo (0)

none

Suggests (6)

knitr rmarkdown devtools testthat seqinr magrittr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Hajk-Georg Drost

Author, Maintainer

Authors (2)

Hajk-Georg Drost

Author, Maintainer

Haakon Tjeldnes

Author, Contributor · added in 1.0.5

Contributors (1)

Haakon Tjeldnes

Author, Contributor · added in 1.0.5

Package Timeline

21 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.7Latest
2023-12-02 · current release · diff ↗
1.0.6
2023-10-24 · diff ↗
1.0.5
2023-10-04 · diff ↗
1.0.4
2023-06-20 · diff ↗
1.0.3
2023-05-07 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.0.2
2022-02-23 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.9.2
2020-01-11 · diff ↗
unarchivedReturned to CRAN
2020-01-10
archivedRemoved from CRAN
2019-12-12
policy violation On Internet access, even on update after being asked to correct

Show 22 earlier events

0.9.1
2019-12-10 · diff ↗
0.9.0
2019-05-21 · diff ↗
unarchivedReturned to CRAN
2019-05-21
archivedRemoved from CRAN
2019-05-19
check problems were not corrected in time
R
R 3.6.0 released · 2019-04-26
0.8.0
2018-06-27 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.7.0
2018-01-03 · diff ↗
0.5.2
2017-09-20 · diff ↗
0.5.1
2017-05-28 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.4.0
2017-03-14 · diff ↗
0.3.0
2017-02-09 · diff ↗
0.2.1
2016-12-15 · diff ↗
0.2.0
2016-11-22 · diff ↗
0.1.0
2016-08-07 · diff ↗
R
R 3.3.0 released · 2016-05-03
0.0.3
2016-03-02 · diff ↗
archivedRemoved from CRAN
2016-01-04
check problems were not corrected despite reminders
0.0.2
2015-08-07 · diff ↗
0.0.1
2015-07-22
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-07-22
Total releases: 21 / 11 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.1.1
Download size: 307 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Report a problem with this page →