Summary
- What does this package do? (explain in 50 words or less):
The biomartr package provides researchers with a useful tool for the efficient, straightforward and reproducible handling of large-scale meta-genomic data from NCBI and ENSEMBL databases and intuitive organism centered interface functions for retrieving functional annotation information from the BioMart database. In general, the package promotes computational reproducibility in genomics studies.
- Paste the full DESCRIPTION file inside a code block below:
Package: biomartr
Title: Genomic Data Retrieval with R
Version: 0.3.0
Author: Hajk-Georg Drost
Maintainer: Hajk-Georg Drost <hgd23@cam.ac.uk>
Description: Perform meta-genomic data retrieval and functional annotation retrieval with
R.
VignetteBuilder: knitr
NeedsCompilation: yes
Depends:
R (>= 3.1.1)
Imports:
biomaRt,
Biostrings,
stringi,
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)
Suggests:
knitr (>= 1.6),
rmarkdown (>= 0.3.3),
devtools (>= 1.6.1),
testthat
License: GPL-3
LazyData: true
URL: https://github.com/HajkD/biomartr
BugReports: https://github.com/HajkD/biomartr/issues
RoxygenNote: 5.0.1
Encoding: UTF-8
- URL for the package (the development repository, not a stylized html page):
https://github.com/HajkD/biomartr
- Who is the target audience?
Life scientists working with genomic data.
- Are there other R packages that accomplish the same thing? If so, what is different about yours?
The R packages seqinr and biomaRt were previous attempts to provide parts of the biomartr functionality. The seqinr package aims to automate sequence retrieval in R but is not designed for meta-genomic approaches and does not include functional annotation. The biomaRt package aims to provide functional annotation methods but these are also not designed for meta-genomic approaches and are not easy to use for non-programming experts. The major advantage of biomartr is that it does not require profound programming expertise and vastly extends the functionality of both packages: seqinr and biomaRt. It is optimized to handle large-scale genomic and meta-genomic data using simple and straightforward commands that are useful for life scientists. The functionality provided by biomartr aims to promote computational reproducibility among life scientists without profound programming expertise. This is not achieved by the packages seqinr and biomaRt which are designed for bioinformaticians and other computationally trained researchers.
Requirements
Confirm each of the following by checking the box. This package:
Publication options
Detail
Is the first submission.
- If possible, please provide recommendations of reviewers - those with experience with similar packages and/or likely users of your package - and their GitHub user names:
None declared.
Summary
The
biomartrpackage provides researchers with a useful tool for the efficient, straightforward and reproducible handling of large-scale meta-genomic data from NCBI and ENSEMBL databases and intuitive organism centered interface functions for retrieving functional annotation information from the BioMart database. In general, the package promotes computational reproducibility in genomics studies.https://github.com/HajkD/biomartr
Life scientists working with genomic data.
The R packages
seqinrandbiomaRtwere previous attempts to provide parts of thebiomartrfunctionality. Theseqinrpackage aims to automate sequence retrieval in R but is not designed for meta-genomic approaches and does not include functional annotation. ThebiomaRtpackage aims to provide functional annotation methods but these are also not designed for meta-genomic approaches and are not easy to use for non-programming experts. The major advantage ofbiomartris that it does not require profound programming expertise and vastly extends the functionality of both packages:seqinrandbiomaRt. It is optimized to handle large-scale genomic and meta-genomic data using simple and straightforward commands that are useful for life scientists. The functionality provided bybiomartraims to promote computational reproducibility among life scientists without profound programming expertise. This is not achieved by the packagesseqinrandbiomaRtwhich are designed for bioinformaticians and other computationally trained researchers.Requirements
Confirm each of the following by checking the box. This package:
Publication options
paper.mdwith a high-level description in the package root or ininst/.Detail
Does
R CMD check(ordevtools::check()) succeed? Paste and describe any errors or warnings:Does the package conform to rOpenSci packaging guidelines? Please describe any exceptions:
If this is a resubmission following rejection, please explain the change in circumstances:
Is the first submission.
None declared.