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RSeqAn

RSeqAn: Headers and wrappers for the SeqAn library in R - Published in JOSS (2019)

https://github.com/compbiocore/rseqan

Science Score: 98.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 8 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ✓
    Committers with academic emails
    1 of 5 committers (20.0%) from academic institutions
  • ✓
    Institutional organization owner
    Organization compbiocore has institutional domain (brown.edu)
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords from Contributors

bioconductor-package

Scientific Fields

Engineering Computer Science - 40% confidence
Last synced: 6 months ago · JSON representation

Repository

SeqAn headers for R

Basic Info
Statistics
  • Stars: 3
  • Watchers: 5
  • Forks: 2
  • Open Issues: 0
  • Releases: 1
Created about 8 years ago · Last pushed almost 5 years ago
Metadata Files
Readme License

README.md

RSeqAn

SeqAn Headers for R

Build Status codecov License Docs DOI

Overview

This package provides R with access to SeqAn v2.4 header files. SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data.

Usage

RSeqAn can be used via the LinkingTo: field in the DESCRIPTION field of an R package. Note that the compiler will need to compile as C++14. This can be done in R as Sys.setenv("PKG_CXXFLAGS"="-std=c++14").

For a quick example, see our introductory vignette. Alternatively you can run the C++ code from the vignette directly by entering

r Rcpp::sourceCpp(system.file("extdata","first_example.cpp",package="RSeqAn")) pattern_search("This is an awesome tutorial to get to know SeqAn!", "tutorial")

Don't forget to set the C++14 compiler flags if you do this!

Installation

  • We recommend installing the release version through Bioconductor, especially if you are running R on Windows. Instructions are provided on their page.

  • Version 1.3.1 can also be installed through Bioconductor (for now, Bioconductor has a separate release cycle), downloaded as a tagged release, or installed with devtools by running: r devtools::install_github("compbiocore/RSeqAn", ref="v1.3.1") This version contains Rcpp::as and Rcpp::wrap functions for CharString and is the one submitted to the Journal of Open Source Software.

  • The development version can be installed with devtools by running: r devtools::install_github("compbiocore/RSeqAn", ref="devel") This version contains additional wrappers, though we cannot guarantee that they will work for you.

Author

August Guang

Release history

See NEWS for release history.

Citation

If you use this package in your work, even if only in auxiliary tools or pipelines please cite:

Guang, (2019). RSeqAn: Headers and wrappers for the SeqAn library in R. Journal of Open Source Software, 4(34), 1160, https://doi.org/10.21105/joss.01160

Please do not forget to cite SeqAn as well:

Reinert, K., Dadi, T. H., Ehrhardt, M., Hauswedell, H., Mehringer, S., Rahn, R., … Weese, D. (2017). The SeqAn C++ template library for efficient sequence analysis: A resource for programmers. Journal of Biotechnology. https://doi.org/10.1016/j.jbiotec.2017.07.017

Owner

  • Name: Computational Biology Core
  • Login: compbiocore
  • Kind: organization
  • Email: cbc-help@brown.edu
  • Location: Providence, RI

Brown University - Center for Computation and Visualization

JOSS Publication

RSeqAn: Headers and wrappers for the SeqAn library in R
Published
February 12, 2019
DOI
Volume 4, Issue 34, Page 1160
Authors
August Guang
Center for Computation and Visualization, Brown University, Providence, Rhode Island, United States of America, Center for Computational Biology of Human Disease, Brown University, Providence, Rhode Island, United States of America
Editor
Roman Valls Guimera ORCID
Tags
SeqAn bioinformatics Rcpp
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GitHub Events

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Last Year

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 85
  • Total Committers: 5
  • Avg Commits per committer: 17.0
  • Development Distribution Score (DDS): 0.165
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
August Guang a****g@g****m 71
aguang a****g@C****l 7
Fernando Gelin f****n@b****u 3
vobencha v****a@g****m 2
vobencha v****n@r****g 2
Committer Domains (Top 20 + Academic)
roswellpark.org: 1 brown.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 2
  • Total pull requests: 0
  • Average time to close issues: 7 months
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
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  • LTLA (1)
  • JulianSpagnuolo (1)
Pull Request Authors
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Dependencies

DESCRIPTION cran
  • Rcpp * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests