[Blends-commit] r2957 - /projects/med/trunk/debian-med/tasks/bio

Wed Sep 14 16:48:27 UTC 2011

Author: tille
Date: Wed Sep 14 16:48:27 2011
New Revision: 2957

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2957
Log:
Added plato

Modified:
    projects/med/trunk/debian-med/tasks/bio

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2957&op=diff
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Wed Sep 14 16:48:27 2011
@@ -3827,6 +3827,51 @@
  what fast mappers will handle gracefully (say the reference genome is missing
  and a related species is used instead).
 
+Depends: plato
+Homepage: https://chgr.mc.vanderbilt.edu/plato
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/plato/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/plato/trunk
+License: GPL-2+
+Pkg-Description: Analysis, translation, and organization of large-scale genetic data
+ PLATO is an acronym for "PLatform for the Analysis, Translation,
+ and Organization of large-scale data".  Recent technological advances
+ enable the study of hundreds of thousands of human single-nucleotide
+ polymorphisms at the population level. Because strategies for analyzing
+ these data have not kept pace with the laboratory methods that generate
+ the data, it is unlikely that these advances will immediately lead to
+ an improved understanding of the genetic contribution to common human
+ disease and drug response. Currently, no single analytical method
+ allows us to extract all available information from a whole-genome
+ association study. In fact, no single method can be optimal for all
+ datasets, especially when the genetic architecture for diseases can
+ vary substantially, as is certainly the case. Therefore, an integrative
+ platform is needed to accommodate multiple analytical methods for
+ analysis as we learn more about genetic architecture. As a result,
+ we are developing a system for the analysis of genome-wide association
+ data that will incorporate several analytical approaches as filters to
+ allow a scientist to choose whatever analytical methods they wish to
+ apply. PLATO (PLatform for the Analysis, Translation, and Organization
+ of large-scale data) will incorporate a number of filters to select
+ the important SNPs in a genome-wide association study.
+ .
+ Whole-genome Association Study Pipeline (WASP) has recently been
+ absorbed into PLATO. WASP was designed to aid in retrieving, evaluating,
+ formatting, and analyzing genotypic and clinical data from the latest
+ large-scale genotyping studies. WASP implements a battery of quality
+ control procedures to assess the data. Among the currently available
+ procedures are the examination of marker and sample genotyping
+ efficiency, allele frequency calculations, checks of Mendelian error
+ (if applicable) and gender discrepancies (based on available chromosome X
+ and Y genotypes), and tests of Hardy-Weinberg Equilibrium. Additionally,
+ WASP can retrieve and format data for other software programs such as the
+ Graphical Representation of Relationships (GRR) program, or STRUCTURE,
+ and depending on the nature of the samples and the depth of examination
+ the user desires to pursue. Beyond the quality control aspect of this
+ application, WASP can perform standard tests of association using the
+ Transmission Disequilibrium Test TDT for family-based datasets and the
+ chi-square test of association for case-control datasets.
+
+
 Comment: Several related R packages are listed at CRAN:
          http://cran.r-project.org/web/views/Genetics.html
 Comment: There is a Gentoo page featuring some projects we do not have mentioned here:


