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', 'ENSEMBLGENOMES', 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. as well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.

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Description file content

Package
biomartr
Title
Genomic Data Retrieval
Version
0.9.0
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', 'ENSEMBLGENOMES', 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. as well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.
VignetteBuilder
knitr
NeedsCompilation
yes
Depends
R (>= 3.1.1)
Imports
biomaRt, Biostrings, curl, tibble, jsonlite, data.table (>= 1.9.4), dplyr (>= 0.3.0), readr (>= 0.2.2), downloader (>= 0.3), RCurl (>= 1.95-4.5), XML (>= 3.98-1.1), httr (>= 0.6.1), stringr (>= 0.6.2), purrr, R.utils, philentropy, fs
Suggests
knitr (>= 1.6), rmarkdown (>= 0.3.3), devtools (>= 1.6.1), testthat, seqinr, magrittr
License
GPL-2
LazyData
true
URL
BugReports
https://github.com/ropensci/biomartr/issues
RoxygenNote
6.1.1
Encoding
UTF-8
X-schema.org-keywords
BioMart, genomic-data-retrieval, annotation-retrieval, database-retrieval, NCBI, ENSEMBL, biological-data-retrieval
X-schema.org-applicationCategory
Data Access
X-schema.org-isPartof
"ropensci.org"
Packaged
2019-05-21 16:38:57 UTC; h-gd
Author
Hajk-Georg Drost [aut, cre] ()
Maintainer
Hajk-Georg Drost
Repository
CRAN
Date/Publication
2019-05-21 17:40:02 UTC

install.packages('biomartr')

0.9.0

a month ago

https://github.com/ropensci/biomartr

Hajk-Georg Drost

GPL-2

Depends on

R (>= 3.1.1)

Imports

biomaRt, Biostrings, curl, tibble, jsonlite, data.table (>= 1.9.4), dplyr (>= 0.3.0), readr (>= 0.2.2), downloader (>= 0.3), RCurl (>= 1.95-4.5), XML (>= 3.98-1.1), httr (>= 0.6.1), stringr (>= 0.6.2), purrr, R.utils, philentropy, fs

Suggests

knitr (>= 1.6), rmarkdown (>= 0.3.3), devtools (>= 1.6.1), testthat, seqinr, magrittr

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