eigensoft_6.1.4+dfsg-1+b1_i386.deb


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Description

eigensoft - reduction of population bias for genetic analyses

Property Value
Distribution Debian 9 (Stretch)
Repository Debian Main i386
Package filename eigensoft_6.1.4+dfsg-1+b1_i386.deb
Package name eigensoft
Package version 6.1.4+dfsg
Package release 1+b1
Package architecture i386
Package type deb
Category science
Homepage http://www.hsph.harvard.edu/faculty/alkes-price/software/
License -
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Download size 356.09 KB
Installed size 2.25 MB
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.

Alternatives

Package Version Architecture Repository
eigensoft_6.1.4+dfsg-1+b1_amd64.deb 6.1.4+dfsg amd64 Debian Main
eigensoft - - -

Requires

Name Value
libblas.so.3 -
libblas3 -
libc6 >= 2.23
libgfortran3 >= 4.3
libgomp1 >= 4.2.1
libgsl2 -
liblapack.so.3 -
liblapack3 -
liblapacke -
perl:any -

Download

Type URL
Mirror ftp.br.debian.org
Binary Package eigensoft_6.1.4+dfsg-1+b1_i386.deb
Source Package eigensoft

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install eigensoft deb package:
    # sudo apt-get install eigensoft

Files

Path
/usr/bin/baseprog
/usr/bin/convertf
/usr/bin/eigenstrat
/usr/bin/eigenstratQTL
/usr/bin/evec2pca
/usr/bin/evec2pca-ped
/usr/bin/gc-eigensoft
/usr/bin/mergeit
/usr/bin/pca
/usr/bin/pcaselection
/usr/bin/pcatoy
/usr/bin/ploteig
/usr/bin/smarteigenstrat
/usr/bin/smartpca
/usr/bin/smartrel
/usr/bin/twstats
/usr/lib/debian-med/bin/evec2pca-ped.perl
/usr/lib/debian-med/bin/evec2pca.perl
/usr/lib/debian-med/bin/gc.perl
/usr/lib/debian-med/bin/smarteigenstrat.perl
/usr/lib/debian-med/bin/smartpca.perl
/usr/lib/eigensoft/smarteigenstrat
/usr/lib/eigensoft/smartpca
/usr/share/doc/eigensoft/README.Debian
/usr/share/doc/eigensoft/README.gz
/usr/share/doc/eigensoft/changelog.Debian.gz
/usr/share/doc/eigensoft/changelog.Debian.i386.gz
/usr/share/doc/eigensoft/copyright
/usr/share/doc/eigensoft/examples/CONVERTF/README.gz
/usr/share/doc/eigensoft/examples/CONVERTF/example.ancestrymapgeno
/usr/share/doc/eigensoft/examples/CONVERTF/example.bed
/usr/share/doc/eigensoft/examples/CONVERTF/example.eigenstratgeno
/usr/share/doc/eigensoft/examples/CONVERTF/example.ind
/usr/share/doc/eigensoft/examples/CONVERTF/example.ind.packedancestrymap
/usr/share/doc/eigensoft/examples/CONVERTF/example.map
/usr/share/doc/eigensoft/examples/CONVERTF/example.packedancestrymap
/usr/share/doc/eigensoft/examples/CONVERTF/example.packedancestrymapgeno
/usr/share/doc/eigensoft/examples/CONVERTF/example.ped
/usr/share/doc/eigensoft/examples/CONVERTF/example.pedind
/usr/share/doc/eigensoft/examples/CONVERTF/example.pedsnp
/usr/share/doc/eigensoft/examples/CONVERTF/example.perl
/usr/share/doc/eigensoft/examples/CONVERTF/example.pheno
/usr/share/doc/eigensoft/examples/CONVERTF/example.snp
/usr/share/doc/eigensoft/examples/CONVERTF/example.snp.packedancestrymap
/usr/share/doc/eigensoft/examples/CONVERTF/ind2pheno.perl
/usr/share/doc/eigensoft/examples/CONVERTF/par.ANCESTRYMAP.EIGENSTRAT
/usr/share/doc/eigensoft/examples/CONVERTF/par.EIGENSTRAT.PED
/usr/share/doc/eigensoft/examples/CONVERTF/par.PACKEDANCESTRYMAP.ANCESTRYMAP
/usr/share/doc/eigensoft/examples/CONVERTF/par.PACKEDPED.PACKEDANCESTRYMAP
/usr/share/doc/eigensoft/examples/CONVERTF/par.PED.EIGENSTRAT
/usr/share/doc/eigensoft/examples/CONVERTF/par.PED.PACKEDPED
/usr/share/doc/eigensoft/examples/EIGENSTRAT/README.gz
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.QTL.chisq
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.QTL.chisq.GC
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.QTL.chisq.par
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.QTL.ind
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.QTL.perl
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.chisq
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.chisq.GC
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.chisq.par
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.eval
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.geno
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.ind
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.log
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.oldstyle.perl
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.pca
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.pca.evec
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.pca.par
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.pcaselection.chisq
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.pcaselection.par
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.perl
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.pheno
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.plot.pdf
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.plot.ps.gz
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.plot.xtxt
/usr/share/doc/eigensoft/examples/EIGENSTRAT/example.snp
/usr/share/doc/eigensoft/examples/POPGEN/HGDP.X.perl
/usr/share/doc/eigensoft/examples/POPGEN/README.gz
/usr/share/doc/eigensoft/examples/POPGEN/example.eval
/usr/share/doc/eigensoft/examples/POPGEN/example.evec
/usr/share/doc/eigensoft/examples/POPGEN/example.geno
/usr/share/doc/eigensoft/examples/POPGEN/example.ind
/usr/share/doc/eigensoft/examples/POPGEN/example.log
/usr/share/doc/eigensoft/examples/POPGEN/example.pca
/usr/share/doc/eigensoft/examples/POPGEN/example.perl
/usr/share/doc/eigensoft/examples/POPGEN/example.plot.pdf
/usr/share/doc/eigensoft/examples/POPGEN/example.plot.ps.gz
/usr/share/doc/eigensoft/examples/POPGEN/example.plot.xtxt
/usr/share/doc/eigensoft/examples/POPGEN/example.plot2.xtxt
/usr/share/doc/eigensoft/examples/POPGEN/example.snp
/usr/share/doc/eigensoft/examples/POPGEN/grmjunk
/usr/share/doc/eigensoft/examples/POPGEN/grmjunk.id
/usr/share/doc/eigensoft/examples/POPGEN/par.example
/usr/share/doc/eigensoft/examples/POPGEN/smartpca.info
/usr/share/doc/eigensoft/examples/POPGEN/twexample.eval
/usr/share/doc/eigensoft/examples/POPGEN/twexample.out.gz
/usr/share/doc/eigensoft/examples/POPGEN/twexample.perl
/usr/share/doc/eigensoft/examples/POPGEN/twtable.gz
/usr/share/eigensoft/CONVERTF/README
/usr/share/eigensoft/CONVERTF/example.ancestrymapgeno
/usr/share/eigensoft/CONVERTF/example.bed
/usr/share/eigensoft/CONVERTF/example.eigenstratgeno
/usr/share/eigensoft/CONVERTF/example.ind
/usr/share/eigensoft/CONVERTF/example.ind.packedancestrymap
/usr/share/eigensoft/CONVERTF/example.map
/usr/share/eigensoft/CONVERTF/example.packedancestrymap
/usr/share/eigensoft/CONVERTF/example.packedancestrymapgeno
/usr/share/eigensoft/CONVERTF/example.ped
/usr/share/eigensoft/CONVERTF/example.pedind
/usr/share/eigensoft/CONVERTF/example.pedsnp
/usr/share/eigensoft/CONVERTF/example.perl
/usr/share/eigensoft/CONVERTF/example.pheno
/usr/share/eigensoft/CONVERTF/example.snp
/usr/share/eigensoft/CONVERTF/example.snp.packedancestrymap
/usr/share/eigensoft/CONVERTF/ind2pheno.perl
/usr/share/eigensoft/CONVERTF/par.ANCESTRYMAP.EIGENSTRAT
/usr/share/eigensoft/CONVERTF/par.EIGENSTRAT.PED
/usr/share/eigensoft/CONVERTF/par.PACKEDANCESTRYMAP.ANCESTRYMAP
/usr/share/eigensoft/CONVERTF/par.PACKEDPED.PACKEDANCESTRYMAP
/usr/share/eigensoft/CONVERTF/par.PED.EIGENSTRAT
/usr/share/eigensoft/CONVERTF/par.PED.PACKEDPED
/usr/share/eigensoft/EIGENSTRAT/README
/usr/share/eigensoft/EIGENSTRAT/example.QTL.chisq
/usr/share/eigensoft/EIGENSTRAT/example.QTL.chisq.GC
/usr/share/eigensoft/EIGENSTRAT/example.QTL.chisq.par
/usr/share/eigensoft/EIGENSTRAT/example.QTL.ind
/usr/share/eigensoft/EIGENSTRAT/example.QTL.perl
/usr/share/eigensoft/EIGENSTRAT/example.chisq
/usr/share/eigensoft/EIGENSTRAT/example.chisq.GC
/usr/share/eigensoft/EIGENSTRAT/example.chisq.par
/usr/share/eigensoft/EIGENSTRAT/example.eval
/usr/share/eigensoft/EIGENSTRAT/example.geno
/usr/share/eigensoft/EIGENSTRAT/example.ind
/usr/share/eigensoft/EIGENSTRAT/example.log
/usr/share/eigensoft/EIGENSTRAT/example.oldstyle.perl
/usr/share/eigensoft/EIGENSTRAT/example.pca
/usr/share/eigensoft/EIGENSTRAT/example.pca.evec
/usr/share/eigensoft/EIGENSTRAT/example.pca.par
/usr/share/eigensoft/EIGENSTRAT/example.pcaselection.chisq
/usr/share/eigensoft/EIGENSTRAT/example.pcaselection.par
/usr/share/eigensoft/EIGENSTRAT/example.perl
/usr/share/eigensoft/EIGENSTRAT/example.pheno
/usr/share/eigensoft/EIGENSTRAT/example.plot.pdf
/usr/share/eigensoft/EIGENSTRAT/example.plot.ps
/usr/share/eigensoft/EIGENSTRAT/example.plot.xtxt
/usr/share/eigensoft/EIGENSTRAT/example.snp
/usr/share/eigensoft/POPGEN/README
/usr/share/eigensoft/POPGEN/example.eval
/usr/share/eigensoft/POPGEN/example.evec
/usr/share/eigensoft/POPGEN/example.geno
/usr/share/eigensoft/POPGEN/example.ind
/usr/share/eigensoft/POPGEN/example.log
/usr/share/eigensoft/POPGEN/example.pca
/usr/share/eigensoft/POPGEN/example.perl
/usr/share/eigensoft/POPGEN/example.plot.pdf
/usr/share/eigensoft/POPGEN/example.plot.ps
/usr/share/eigensoft/POPGEN/example.plot.xtxt
/usr/share/eigensoft/POPGEN/example.plot2.xtxt
/usr/share/eigensoft/POPGEN/example.snp
/usr/share/eigensoft/POPGEN/grmjunk
/usr/share/eigensoft/POPGEN/grmjunk.id
/usr/share/eigensoft/POPGEN/par.example
/usr/share/eigensoft/POPGEN/smartpca.info
/usr/share/eigensoft/POPGEN/twexample.eval
/usr/share/eigensoft/POPGEN/twexample.out
/usr/share/eigensoft/POPGEN/twexample.perl
/usr/share/eigensoft/POPGEN/twtable
/usr/share/man/man1/smarteigenstrat.1.gz

Changelog

2016-10-16 - Andreas Tille <tille@debian.org>
eigensoft (6.1.4+dfsg-1) unstable; urgency=medium
* New upstream version
* fix perl interpreter path
2016-08-05 - Andreas Tille <tille@debian.org>
eigensoft (6.1.3+dfsg-1) unstable; urgency=medium
* New upstream version
* Upstream has changed extensions from .pl to .perl
2016-07-19 - Andreas Tille <tille@debian.org>
eigensoft (6.1.2+dfsg-1) unstable; urgency=medium
[ Andreas Tille ]
* New upstream version
* Adapt watch file to match new version string
* relicense Debian packaging as BSD-3-clause
* cme fix dpkg-control
* hardening=+bindnow
* Leave only wrapper scripts in /usr/bin, executables go to /usr/lib/eigensoft
* add at least one manpage
* add examples
[ Tatiana Malygina ]
* Fix headers
2016-02-07 - Andreas Tille <tille@debian.org>
eigensoft (6.0.1+ds-1) unstable; urgency=medium
[ Andreas Tille ]
* New upstream version
* Fixed d/watch
* Use Files-Excluded to strip upstream source
* Cleanup d/rules
* Moved packaging from SVN to Git
* cme fix dpkg-control
* Priority: optional
* debhelper 9
* Remove -dbg package which is autogenerated now
* DEP3 header and removed unused patches
* Removed README.Debian which is not user oriented
* Add missing Build-Depends libgsl-dev
* Propagate hardening options
* Fix permission of some Perl scripts
* Remove dubious non-perl script consisting from comment only
[ Petter Reinholdtsen ]
* Added lapacke.patch to link with -llapacke and -llapack.
* Added liblapacke-dev as build-dependency.
* Added a simple autopkgtest script to verify that at least some of the
binaries are able to run.
2011-09-15 - Steffen Moeller <moeller@debian.org>
eigensoft (4.2-1) experimental; urgency=low
* New upstream release.
2011-09-14 - Steffen Moeller <moeller@debian.org>
eigensoft (3.0-1) UNRELEASED; urgency=low
* Initial release (Closes: #641724).

See Also

Package Description
einstein_2.0.dfsg.2-9+b2_i386.deb Puzzle game inspired on Einstein's puzzle
eiskaltdcpp-cli_2.2.9-4.1_all.deb EiskaltDC++ command-line interface
eiskaltdcpp-common_2.2.9-4.1_all.deb common files for EiskaltDC++
eiskaltdcpp-daemon_2.2.9-4.1_i386.deb EiskaltDC++ daemon
eiskaltdcpp-emoticons_2.2.9-4.1_all.deb emoticons for EiskaltDC++
eiskaltdcpp-gtk-data_2.2.9-4.1_all.deb data files for EiskaltDC++ Gtk
eiskaltdcpp-gtk3_2.2.9-4.1_i386.deb EiskaltDC++ GUI on Gtk3
eiskaltdcpp-gtk_2.2.9-4.1_i386.deb EiskaltDC++ GUI on Gtk
eiskaltdcpp-qt-data_2.2.9-4.1_all.deb data files for EiskaltDC++ Qt
eiskaltdcpp-qt-mini_2.2.9-4.1_i386.deb EiskaltDC++ GUI on Qt (stripped-down version)
eiskaltdcpp-qt_2.2.9-4.1_i386.deb EiskaltDC++ GUI on Qt
eiskaltdcpp-scripts_2.2.9-4.1_all.deb scripts examples for EiskaltDC++
eiskaltdcpp-sounds_2.2.9-4.1_all.deb sound files for EiskaltDC++
eiskaltdcpp_2.2.9-4.1_all.deb EiskaltDC++ metapackage
eja_9.5.20-1_i386.deb micro web server for static and dynamic Lua generated content
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