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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 ```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`](/inst/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, 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.