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ProbABEL package

ProbABEL

Genome-wide association analysis of imputed data
  • Status: Stable
  • Installation:
    • Compile ProbABEL from source: Download the source code and unpack (tar -xzf probabel-0.3.0.tar.gz). Then read the instructions in the /doc/INSTALL file. The signature files can be used to verify that the files identical to the original and have not been tampered with (e.g. run gpg --verify probabel-0.3.0.tar.gz.asc). [ stable source code, GPG signature ].
    • .deb packages: If you are running Ubuntu (or one of its derivative distributions like Kubuntu or Linux Mint) or Debian Linux, take a look at the GenABEL PPA for easy installation of the ProbABEL package. Basically it boils down to following these steps:
      sudo add-apt-repository ppa:l.c.karssen/genabel-ppa
      sudo apt-get update
      sudo apt-get install probabel
    • Pre-compiled binaries for Windows: The following links point to zip files with ready-to-run Windows binaries for both 32 bit and 64 bit Windows. Please note that we haven't tested these (since most people doing large GWAS run on Linux clusters/servers). [ Win64 binary, GPG signature | Win32 binary, GPG signature ]. The signature files can be used to verify that the files identical to the original and have not been tampered with (e.g. run gpg --verify probabel-0.3.0-Win32.zip.asc).
  • Cox PH module: Unfortunately the Cox Proportional Hazards module in ProbBEL v.0.3.0 is broken. ProbABEL v.0.1-3 provides a working version, which unfortunately does not work with files in DatABEL format. [ Stable source code for Cox PH ]. Install instructions can be found in the file doc/INSTALL in the .tar.gz file.
  • Quick start: after installation: cd examples; sh example_all.sh
  • Tutorial: would someone like to contribute one?
  • Manual: [ PDF | HTML ] (please note that the PDF version is usually more up-to-date than the HTML version)
  • Reference: ProbABEL package for genome-wide association analysis of imputed data
  • Known issues: see our bug tracker
  • Financial support: Development of this package was financially supported by grants from the Centre for Medical Systems Biology (CMSB), The Netherlands; the Netherlands Genomics Initiative (NGI), the Netherlands Organisation for Scientific Research (NWO), the Radboud University Medical Centre, Nijmegen, The Netherlands and the Russian Foundation for Basic Research (RFBR).