Description
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:
- does not violate the Terms of Service of any service it interacts with.
- has a CRAN and OSI accepted license.
- contains a README with instructions for installing the development version.
- includes documentation with examples for all functions.
- contains a vignette with examples of its essential functions and uses.
- has a test suite.
- has continuous integration with Travis CI and/or another service.
Publication options
- Do you intend for this package to go on CRAN? (is already on CRAN)
- Do you wish to automatically submit to the Journal of Open Source Software? If so:
- The package contains a
paper.mdwith a high-level description in the package root or ininst/. - The package is deposited in a long-term repository with the DOI:
- (Do not submit your package separately to JOSS)
- The package contains a
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.
- 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.