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Re-implementation of R/qtl with clean code, aimed at high-density, high-throughput data

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README.md

R/qtlHD

R/qtlHD (or qtlHD) is the next generation implementation of R/qtl. qtlHD is aimed at QTL analysis of high-density, high-throughput data; for example for RNA-seq.

Features

  • qtlHD is written in the high performance D language. D is a modern strictly typed compiled language with great support for concurrency. D can be bound against R, Ruby, Python, Perl, etc. D runs on Linux, OS/X and Windows.
  • qtlHD currently does scanone
  • qtlHD comes with a new flexible data standard for QTL mapping, named qtab. Qtab should be able to describe most datasets, see qtab documentation.

Compiling qtlHD

To compile qtlHD a recent edition of the D compiler is needed, currently:

DMD64 D Compiler v2.063

After D installation, build and test (which needs rake):

./test_all.sh

for more information see INSTALL.md

Platforms

qtlHD is developed and tested on Mac OS X, Microsoft Windows and Debian Linux.

TODO

Before a full release:

  • Create a standalone executable for scanone
  • Create an interface for R and bioruby.

Issues

qtlHD has an issue tracker on github.

License

qtlHD source code is published under the liberal open source BSD License - see the LICENSE file in the source tree.

Source code

The source code for qtlHD can be found on github.

Contributors

  • Karl W. Broman
  • Pjotr Prins
  • Danny Arends
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