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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

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:

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:
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