NDLI: Biomartr: genomic data retrieval with R

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Biomartr: genomic data retrieval with R

Content Provider	Semantic Scholar
Author	Drost, Hajk-Georg Paszkowski, Jerzy
Copyright Year	2017
Abstract	Motivation Retrieval and reproducible functional annotation of genomic data are crucial in biology. However, the current poor usability and transparency of retrieval methods hinders reproducibility. Here we present an open source R package, biomartr , which provides a comprehensive easy-to-use framework for automating data retrieval and functional annotation for meta-genomic approaches. The functions of biomartr achieve a high degree of clarity, transparency and reproducibility of analyses. Results The biomartr package implements straightforward functions for bulk retrieval of all genomic data or data for selected genomes, proteomes, coding sequences and annotation files present in databases hosted by the National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EMBL-EBI). In addition, biomartr communicates with the BioMart database for functional annotation of retrieved sequences. Comprehensive documentation of biomartr functions and five tutorial vignettes provide step-by-step instructions on how to use the package in a reproducible manner. Availability and Implementation The open source biomartr package is available at https://github.com/HajkD/biomartr and https://cran.r-project.org/web/packages/biomartr/index.html . Contact hgd23@cam.ac.uk. Supplementary information Supplementary data are available at Bioinformatics online.
Starting Page	1216
Ending Page	1217
Page Count	2
File Format	PDF HTM / HTML
Alternate Webpage(s)	https://www.wikidata.org/entity/Q31155793
PubMed reference number	28110292v1
Alternate Webpage(s)	https://doi.org/10.1093/bioinformatics/btw821
DOI	10.1093/bioinformatics/btw821
Journal	Bioinformatics
Volume Number	33
Language	English
Access Restriction	Open
Subject Keyword	Annotation BioMart Bioinformatics Clarity Measurement Data retrieval Documentation External Bus Interface Genome Geographic Information Systems NCBI Taxonomy National Center for Biotechnology Information Open-source software Proteome Published Database R language Usability
Content Type	Text
Resource Type	Article

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