1. RSeqAn
  2. README.md
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august authored on 12/02/2019 20:16:46 • GitHub committed on 12/02/2019 20:16:46
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README.md
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2 2 
 SeqAn Headers for R
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4 4 
 [![Build Status](https://travis-ci.org/compbiocore/RSeqAn.svg?branch=master)](https://travis-ci.org/compbiocore/RSeqAn) [![codecov](https://codecov.io/gh/compbiocore/RSeqAn/branch/master/graph/badge.svg)](https://codecov.io/gh/compbiocore/RSeqAn) [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
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+[![Docs](https://img.shields.io/badge/docs-stable-steelblue.svg?style=flat-square)](https://compbiocore.github.io/RSeqAn)
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+[![DOI](http://joss.theoj.org/papers/10.21105/joss.01160/status.svg)](https://doi.org/10.21105/joss.01160)
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 ## Overview
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@@ -46,7 +48,10 @@ See [`NEWS`](/inst/NEWS) for release history.
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 ## Citation
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-To cite this package from within R, enter `citation("RSeqAn")`. Citation is also provided below:
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-	Guang A (2018). *RSeqAn: R SeqAn.* R package version 1.3.1.
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+If you use this package in your work, even if only in auxiliary tools or pipelines please cite:
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-Please do not forget to cite SeqAn if you use this package in your acedemic work, even if only in auxiliary tools or pipelines: https://doi.org/10.1016/j.jbiotec.2017.07.017
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+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
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+
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+Please do not forget to cite SeqAn as well:
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+
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+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
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Update README.md

august authored on 05/02/2019 18:08:50 • GitHub committed on 05/02/2019 18:08:50
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README.md
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@@ -24,7 +24,7 @@ Don't forget to set the C++14 compiler flags if you do this!
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  * We recommend installing the release version [through Bioconductor](https://bioconductor.org/packages/release/bioc/html/RSeqAn.html), especially if you are running R on Windows. Instructions are provided on their page.
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- * Version 1.3.1 can also be installed [through Bioconductor](http://bioconductor.org/packages/devel/bioc/html/RSeqAn.html), downloaded as [a tagged release](https://github.com/compbiocore/RSeqAn/releases/tag/v1.3.1), or installed with `devtools` by running:
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+ * Version 1.3.1 can also be installed [through Bioconductor](http://bioconductor.org/packages/devel/bioc/html/RSeqAn.html) (for now, Bioconductor has a separate release cycle), downloaded as [a tagged release](https://github.com/compbiocore/RSeqAn/releases/tag/v1.3.1), or installed with `devtools` by running:
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 ```r
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 devtools::install_github("compbiocore/RSeqAn", ref="v1.3.1")
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 ```
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Update README.md

august authored on 05/02/2019 18:02:01 • GitHub committed on 05/02/2019 18:02:01
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README.md
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@@ -22,15 +22,15 @@ Don't forget to set the C++14 compiler flags if you do this!
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23 23 
 ## Installation
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-We recommend installing the release version [through Bioconductor](https://bioconductor.org/packages/release/bioc/html/RSeqAn.html), especially if you are running R on Windows. Instructions are provided on their page.
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+ * We recommend installing the release version [through Bioconductor](https://bioconductor.org/packages/release/bioc/html/RSeqAn.html), especially if you are running R on Windows. Instructions are provided on their page.
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-Version 1.3.1 can also be installed [through Bioconductor](http://bioconductor.org/packages/devel/bioc/html/RSeqAn.html), downloaded as [a tagged release](https://github.com/compbiocore/RSeqAn/releases/tag/v1.3.1), or installed with `devtools` by running:
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+ * Version 1.3.1 can also be installed [through Bioconductor](http://bioconductor.org/packages/devel/bioc/html/RSeqAn.html), downloaded as [a tagged release](https://github.com/compbiocore/RSeqAn/releases/tag/v1.3.1), or installed with `devtools` by running:
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 ```r
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 devtools::install_github("compbiocore/RSeqAn", ref="v1.3.1")
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 ```
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 This version contains `Rcpp::as` and `Rcpp::wrap` functions for `CharString` and is the one submitted to the [Journal of Open Source Software](https://joss.theoj.org/).
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-The development version can be installed with `devtools` by running:
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+ * The development version can be installed with `devtools` by running:
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 ```r
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 devtools::install_github("compbiocore/RSeqAn", ref="devel")
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 ```
Browse code

Update README.md

august authored on 05/02/2019 18:01:18 • GitHub committed on 05/02/2019 18:01:18
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README.md
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@@ -22,13 +22,19 @@ Don't forget to set the C++14 compiler flags if you do this!
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 ## Installation
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-We recommend installing the release version [through Bioconductor](https://bioconductor.org/packages/release/bioc/html/RSeqAn.html). Instructions are provided on their page.
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+We recommend installing the release version [through Bioconductor](https://bioconductor.org/packages/release/bioc/html/RSeqAn.html), especially if you are running R on Windows. Instructions are provided on their page.
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-If you have `devtools`, then the development version can be installed from here by running:
27 
+Version 1.3.1 can also be installed [through Bioconductor](http://bioconductor.org/packages/devel/bioc/html/RSeqAn.html), downloaded as [a tagged release](https://github.com/compbiocore/RSeqAn/releases/tag/v1.3.1), or installed with `devtools` by running:
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 ```r
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-devtools::install_github("compbiocore/RSeqAn")
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+devtools::install_github("compbiocore/RSeqAn", ref="v1.3.1")
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 ```
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-The development version contains `Rcpp::as` and `Rcpp::wrap` functions for `CharString`.
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+This version contains `Rcpp::as` and `Rcpp::wrap` functions for `CharString` and is the one submitted to the [Journal of Open Source Software](https://joss.theoj.org/).
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+
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+The development version can be installed with `devtools` by running:
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+```r
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+devtools::install_github("compbiocore/RSeqAn", ref="devel")
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+```
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+This version contains additional wrappers, though we cannot guarantee that they will work for you.
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 ## Author
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Browse code

Update README.md

added link to vignette as well as direct c++ code in usage

august authored on 05/02/2019 16:53:16 • GitHub committed on 05/02/2019 16:53:16
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README.md
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@@ -11,6 +11,15 @@ This package provides R with access to [SeqAn v2.4](http://www.seqan.de/) header
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 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")`.
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+For a quick example, see our [introductory vignette](https://compbiocore.github.io/RSeqAn/first_example/). Alternatively you can run the C++ code from the vignette directly by entering
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+
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+```r
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+Rcpp::sourceCpp(system.file("extdata","first_example.cpp",package="RSeqAn"))
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+pattern_search("This is an awesome tutorial to get to know SeqAn!", "tutorial")
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+```
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+
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+Don't forget to set the C++14 compiler flags if you do this!
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+
14 23 
 ## Installation
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 We recommend installing the release version [through Bioconductor](https://bioconductor.org/packages/release/bioc/html/RSeqAn.html). Instructions are provided on their page.
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@@ -19,7 +28,7 @@ If you have `devtools`, then the development version can be installed from here
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 ```r
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 devtools::install_github("compbiocore/RSeqAn")
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 ```
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-This version contains `Rcpp::as` and `Rcpp::wrap` functions for `CharString`.
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+The development version contains `Rcpp::as` and `Rcpp::wrap` functions for `CharString`.
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 ## Author
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 ## Citation
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 To cite this package from within R, enter `citation("RSeqAn")`. Citation is also provided below:
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-	Guang A (2018). *RSeqAn: R SeqAn.* R package version 1.2.0.
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+	Guang A (2018). *RSeqAn: R SeqAn.* R package version 1.3.1.
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-Please do not forget to cite SeqAn if you use this package in your acedemic work, even if only in auxiliary tools or pipelines: https://doi.org/10.1016/j.jbiotec.2017.07.017
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\ No newline at end of file
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+Please do not forget to cite SeqAn if you use this package in your acedemic work, even if only in auxiliary tools or pipelines: https://doi.org/10.1016/j.jbiotec.2017.07.017
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updated NEWS, README, DESCRIPTION to go with bioconductor devel

August Guang authored on 29/11/2018 20:18:03
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1 
-[![Build Status](https://travis-ci.org/compbiocore/RSeqAn.svg?branch=master)](https://travis-ci.org/compbiocore/RSeqAn) [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
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-
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 # RSeqAn
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 SeqAn Headers for R
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-## About
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+[![Build Status](https://travis-ci.org/compbiocore/RSeqAn.svg?branch=master)](https://travis-ci.org/compbiocore/RSeqAn) [![codecov](https://codecov.io/gh/compbiocore/RSeqAn/branch/master/graph/badge.svg)](https://codecov.io/gh/compbiocore/RSeqAn) [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
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+
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+## Overview
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 This package provides R with access to [SeqAn v2.4](http://www.seqan.de/) 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.
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+## Usage
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+
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 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")`.
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+## Installation
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+
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+We recommend installing the release version [through Bioconductor](https://bioconductor.org/packages/release/bioc/html/RSeqAn.html). Instructions are provided on their page.
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+
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+If you have `devtools`, then the development version can be installed from here by running:
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+```r
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+devtools::install_github("compbiocore/RSeqAn")
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+```
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+This version contains `Rcpp::as` and `Rcpp::wrap` functions for `CharString`.
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+
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 ## Author
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 August Guang
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+## Release history
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+
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+See [`NEWS`](/inst/NEWS) for release history.
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+
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 ## Citation
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+To cite this package from within R, enter `citation("RSeqAn")`. Citation is also provided below:
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+	Guang A (2018). *RSeqAn: R SeqAn.* R package version 1.2.0.
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+
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 Please do not forget to cite SeqAn if you use this package in your acedemic work, even if only in auxiliary tools or pipelines: https://doi.org/10.1016/j.jbiotec.2017.07.017
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\ No newline at end of file
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got up to getuid

August Guang authored on 05/03/2018 15:54:34
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@@ -11,4 +11,8 @@ RSeqAn can be used via the `LinkingTo:` field in the `DESCRIPTION` field of an R
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 ## Author
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-August Guang
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\ No newline at end of file
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+August Guang
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+
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+## Citation
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+
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+Please do not forget to cite SeqAn if you use this package in your acedemic work, even if only in auxiliary tools or pipelines: https://doi.org/10.1016/j.jbiotec.2017.07.017
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\ No newline at end of file
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defined mingw64 macros

August Guang authored on 21/02/2018 16:37:44
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-[![Build Status](https://travis-ci.org/compbiocore/RSeqAn.svg?branch=master)](https://travis-ci.org/compbiocore/RSeqAn) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
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+[![Build Status](https://travis-ci.org/compbiocore/RSeqAn.svg?branch=master)](https://travis-ci.org/compbiocore/RSeqAn) [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
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 # RSeqAn
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 SeqAn Headers for R
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added vignettes, updated license

August Guang authored on 19/02/2018 16:00:55
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-[![Build Status](https://travis-ci.org/compbiocore/RSeqAn.svg?branch=master)](https://travis-ci.org/compbiocore/RSeqAn) [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
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+[![Build Status](https://travis-ci.org/compbiocore/RSeqAn.svg?branch=master)](https://travis-ci.org/compbiocore/RSeqAn) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
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 # RSeqAn
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 SeqAn Headers for R
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 ## Author
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-August Guang
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-
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-## License
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-
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-The license provided is the same as for SeqAn and is unaltered.
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\ No newline at end of file
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+August Guang
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\ No newline at end of file
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updated license, README

aguang authored on 16/02/2018 15:15:15
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-[![Build Status](https://travis-ci.org/compbiocore/RSeqAn.svg?branch=master)](https://travis-ci.org/compbiocore/RSeqAn)
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+[![Build Status](https://travis-ci.org/compbiocore/RSeqAn.svg?branch=master)](https://travis-ci.org/compbiocore/RSeqAn) [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
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-# RseqAn
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-SeqAn for R
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+# RSeqAn
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+SeqAn Headers for R
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+
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+## About
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+
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+This package provides R with access to [SeqAn v2.4](http://www.seqan.de/) 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.
9 
+
10 
+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")`.
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+
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+## Author
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+
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+August Guang
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+
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+## License
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+
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+The license provided is the same as for SeqAn and is unaltered.
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\ No newline at end of file
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added travis badge

aguang authored on 15/02/2018 14:34:36
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+[![Build Status](https://travis-ci.org/compbiocore/RSeqAn.svg?branch=master)](https://travis-ci.org/compbiocore/RSeqAn)
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+
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 # RseqAn
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 SeqAn for R
Browse code

Initial commit

august authored on 13/02/2018 16:21:05 • GitHub committed on 13/02/2018 16:21:05
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README.md
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+# RseqAn
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+SeqAn for R