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Bug#641724: RFP: eigensoft -- reduction of statistical effects by population co-inheritance



Package: wnpp
Severity: wishlist

* Package name    : eigensoft
  Version         : 4.2
* URL             : http://www.hsph.harvard.edu/faculty/alkes-price/software/
* License         : non-free but redistributable
  Programming Lang: C, Perl
  Description     : reduction of statistical effects by population co-inheritance

 The EIGENSOFT package combines functionality from the group's population
 genetics methods (Patterson et al. 2006) and their EIGENSTRAT stratification
 method (Price et al. 2006). The EIGENSTRAT method uses principal components
 analysis to explicitly model ancestry differences between cases and
 controls along continuous axes of variation; the resulting correction is
 specific to a candidate marker's variation in frequency across ancestral
 populations, minimizing spurious associations while maximizing power to
 detect true associations. The EIGENSOFT package has a built-in plotting
 script and supports multiple file formats and quantitative phenotypes.

 The package is mostly ready at 
	http://anonscm.debian.org/viewvc/debian-med/trunk/packages/eigensoft/trunk/
 of the Debian Med repository. It still has a series of lintian errors

	W: eigensoft source: dbg-package-missing-depends eigensoft-dbg
	W: eigensoft: new-package-should-close-itp-bug
	W: eigensoft: wrong-bug-number-in-closes l3:#nnnn
	E: eigensoft: helper-templates-in-copyright
	E: eigensoft: helper-templates-in-copyright
	E: eigensoft: helper-templates-in-copyright
	W: eigensoft: copyright-has-url-from-dh_make-boilerplate
	E: eigensoft: copyright-contains-dh_make-todo-boilerplate
	W: eigensoft: binary-without-manpage usr/bin/baseprog
	W: eigensoft: binary-without-manpage usr/bin/convertf
	W: eigensoft: binary-without-manpage usr/bin/eigenstrat
	W: eigensoft: binary-without-manpage usr/bin/eigenstrat.big.perl
	W: eigensoft: binary-without-manpage usr/bin/eigenstratQTL
	W: eigensoft: binary-without-manpage usr/bin/eigenstratQTL.big.perl
	W: eigensoft: binary-without-manpage usr/bin/evec2pca.perl
	W: eigensoft: binary-without-manpage usr/bin/fixgreen
	W: eigensoft: binary-without-manpage usr/bin/gc.perl
	W: eigensoft: binary-without-manpage usr/bin/mergeit
	W: eigensoft: binary-without-manpage usr/bin/pca
	W: eigensoft: binary-without-manpage usr/bin/pcatoy
	W: eigensoft: binary-without-manpage usr/bin/ploteig
	W: eigensoft: binary-without-manpage usr/bin/smarteigenstrat
	W: eigensoft: binary-without-manpage usr/bin/smarteigenstrat.perl
	W: eigensoft: binary-without-manpage usr/bin/smartpca
	W: eigensoft: binary-without-manpage usr/bin/smartpca.perl
	W: eigensoft: binary-without-manpage usr/bin/smartrel
	W: eigensoft: binary-without-manpage usr/bin/twstats
	W: eigensoft: unusual-interpreter usr/share/eigenstrat/POPGEN/HGDP.X.perl #!/usr/bin
	W: eigensoft-dbg: new-package-should-close-itp-bug
	W: eigensoft-dbg: wrong-bug-number-in-closes l3:#nnnn
	E: eigensoft-dbg: helper-templates-in-copyright
	E: eigensoft-dbg: helper-templates-in-copyright
	E: eigensoft-dbg: helper-templates-in-copyright
	W: eigensoft-dbg: copyright-has-url-from-dh_make-boilerplate
	E: eigensoft-dbg: copyright-contains-dh_make-todo-boilerplate

 and needs the OK by upstream, still.



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