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PeakSegPipeline on CRAN
There are many R packages for ChIP-seq data analysis, which is important in genomics. One such package is PeakSegPipeline, which implements state-of-the-art machine learning algorithms for highly accurate peak detection. PeakSegPipeline is working on Ubuntu, and the goal of this project is to port PeakSegPipeline to Windows/Mac to get it ready for a CRAN submission.
TODO list related PeakSeg packages and BioC pkgs.
Detailed project goals:
- setup Appveyor-CI to test on windows and mac.
- create/document installation procedure for windows/mac.
- identify GNU/Linux-specific code, e.g.
fread("tail -1 coverage.bedGraph"), and modify so that it works on windows/mac. - use R-hub to check on Mac and Win-Builder to check on windows.
The ideal student will also write tests, documentation, vignettes and a blog.
This GSOC project will make the PeakSegPipeline package more portable, so that this important code can be used on a wider variety of systems, and installed easily from CRAN.
Please get in touch with Toby Dylan Hocking <[email protected]> after completing at least one of the tests below.
Easy: download the PeakSegPipeline package and run test-pipeline-demo.R on your own computer.
Medium: demonstrate that you know how to use docker images, which you will need to use in GSOC to test PeakSegPipeline on different systems. Inside of a windows docker image, try installing PeakSegPipeline – what happens?
Hard: look through the source code and explain which parts you think will need to be changed so that the code works on Win/Mac.
- Students, please post a link to your test results here.