The mission of the GenABEL project is to provide a free framework for collaborative, robust, transparent, open-source based development of statistical genomics methodology. We aim to streamline methodology discussion, development, implementation, dissemination and maintenance; through the community.

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ProbABEL v0.4.4 released

The ProbABEL development team is happy to announce the release of ProbABEL v0.4.4. This release is a bugfix update. People using the Cox Proportional Hazards regression module are strongly advised to upgrade.
(Please click on "read more", below, for more details.)

DatABEL v.0.9-5 published on CRAN

A new version of DatABEL has just been published on CRAN.

The most important changes in DatABEL v0.9-5 are two fixed bugs:
- Fixed bug #5793: impute2DatABEL gives several errors
- Fixed bug #1126: Using mach2databel() or impute2mach() to convert files to the filevector format leaves fvtmp files behind

More open than ever: the source code, the manuscript, the review

Last week, the manuscript describing algorithms and implementation of the OmicABEL package became available online via f1000research, and was assigned doi:10.12688/f1000research.4867.1. Publishing in f1000research - "The first Open Science journal for life scientists" - is a natural step for the GenABEL project, which practices open source/methods/science ideology. In f1000research, manuscripts are published immediately, followed by post-publication open (non-anonymous) review. If two reviewers approve the manuscript, it is then indexed in PubMed, Scopus and Web-Of-Science. [Please click on 'READ MORE' below for complete story]

ProbABEL v0.4.3 released

The ProbABEL development team is happy to announce the release of ProbABEL v0.4.3. This release is a minor update, mostly speeding up reading filevector data.
Information on how to get the source code or binaries can be found on the ProbABEL page.

The most important user-visible changes are:
1) Speed-up of a factor of ~ 2 for linear, logistic and Cox regression when using input files in filevector format.
2) Improved documentation on the installation procedure in the ProbABEL manual.

Thanks to all who made this release possible, by providing code patches, by being beta testers, by suggesting enhancements, or otherwise.
(Please click on "read more", below, for more details.)

MetABEL v0.2-0 available on CRAN

Version 0.2-0 of MetABEL has just been released on CRAN. This version contains fixes to the forest plots.
(Please click on "read more", below, for more details.)

MetABEL v0.1-0 available on CRAN

Today MetABEL version 0.1-0 was accepted on CRAN. This version contains mostly small fixes needed to keep the package accepted by CRAN. The only user-visible changes are in the documentation where several lines that were too long have been made to fit within the margins.

If you run into any bugs please let us know in our bug tracker. For support questions, please use the GenABEL forum.

ProbABEL v0.4.2 released

The ProbABEL development teams is happy to announce the release of ProbABEL v0.4.2. Information on how to get the source code or binaries can be found on the ProbABEL page.

The most important user-visible changes are:
1) Starting with this release the probabel.pl wrapper script has been renamed to probabel. In order not to disrupt any current pipelines a symbolic link is created to the old name. When the user invokes the script with the old name a warning will be printed to encourage them to use the new name. The old name will remain available for several future releases, but will be removed at some point.
2) Improved convergence checks for the Cox PH regression module
3) Fixed a bug where ProbABEL crashed when having large indels in the info file

Thanks to all who made this release possible, by providing code patches, by being beta testers, by suggesting enhancements, or otherwise.
(Please click on "read more", below, for more details.)

ProbABEL v0.4.1 packaged in Debian Unstable

We are happy to announce that ProbABEL has been packaged for Debian and is now available in Debian Unstable. This means that ProbABEL will be available in the next Debian release and also in upcoming releases of Ubuntu, Linux Mint and other Debian derivatives.
Many thanks to the people of the Debian Med team, especially Andreas Tille, who mentored the packaging process.

Genomic control for non-additive models

A manuscript on "Development and application of genomic control methods for genome-wide association studies using non-additive models" was recently published on-line (PLOS ONE). The work reported in the manuscript extends the genomic control method to non-additive models; all methods are implemented in GenABEL.

(To continue reading this story click on 'read more' below.)

Improvements in GenABEL development: continuous integration testing

GenABEL development has made a big step forward with the use of the Jenkins continuous integration platform. Our Jenkins server automatically runs a series of checks each time a change in the code is committed to our SVN version control system. This enables us to continuously monitor the health of our code base by running static code analysis, checks for memory leaks, adherence to coding standards, etc. Hopefully this increases both the stability and the maintainability of the code.

(To continue reading this story click on 'read more' below.)

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