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Balík: pique (1.0-3)

software pipeline for performing genome wide association studies

PIQUE is a software pipeline for performing genome wide association studies (GWAS). The main function of PIQUE is to provide ‘convenience’ wrappers that allow users to perform GWAS using the popular program EMMAX (Kang et al., 2010) without the need to be familiar with all of the software tools used to generate the required EMMAX input files. PIQUE will also perform a number of quality control steps prior to running EMMAX, ensuring that the various input data files are in the correct format. PIQUE proceeds in two main stages although there are multiple entry and exit points from which the pipeline can be run. The first stage consists of running the “pique-input” program, which can read genotype and phenotype information in several different formats and generates all the necessary input files required to run EMMAX. The second step in the pipeline uses the “pique-run” program to actually run EMMAX using the files generated by “pique-input” (or pre-existing user-supplied input files) to perform the GWAS and output the analysis summary files.

Ostatné balíky súvisiace s balíkom pique

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  • odporúča
  • navrhuje
  • dep: eigensoft
    reduction of population bias for genetic analyses
  • dep: emmax
    genetic mapping considering population structure
  • dep: libfile-slurp-perl
    single call read & write file routines
  • dep: libparallel-forkmanager-perl
    simple parallel processing fork manager for Perl
  • dep: libreadonly-perl
    facility for creating read-only scalars, arrays and hashes
  • dep: perl
    Larry Wall's Practical Extraction and Report Language
  • dep: plink
    whole-genome association analysis toolset
  • dep: r-base-core
    GNU R core of statistical computation and graphics system
  • dep: r-cran-forecast
    GNU R forecasting functions for time series and linear models
  • dep: r-cran-getopt
    GNU R package providing command-line parsing functionality
  • dep: r-cran-optparse
    GNU/R Command line option parser
  • dep: r-cran-uroot
    GNU R unit root tests for seasonal time series

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