perl-GO-TermFinder-0.86-alt6_10.x86_64.rpm


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Description

perl-GO-TermFinder - Identify GO nodes that annotate a group of genes with a significant p-value

Property Value
Distribution ALT Linux Sisyphus
Repository Autoimports x86_64
Package filename perl-GO-TermFinder-0.86-alt6_10.x86_64.rpm
Package name perl-GO-TermFinder
Package version 0.86
Package release alt6_10
Package architecture x86_64
Package type rpm
Category Development/Other
Homepage -
License -
Maintainer -
Download size 396.52 KB
Installed size 396.52 KB
This package is intended to provide a method whereby the P-values of a set
of GO annotations can be determined for a set of genes, based on the number
of genes that exist in the particular genome (or in a selected background
distribution from the genome), and their annotation, and the frequency with
which the GO nodes are annotated across the provided set of genes. The
P-value is simply calculated using the hypergeometric distribution as the
probability of x or more out of n genes having a given annotation, given
that G of N have that annotation in the genome in general. We chose the
hypergeometric distribution (sampling without replacement) since it is more
accurate, though slower to calculate, than the binomial distribution
(sampling with replacement).

Alternatives

Package Version Architecture Repository
perl-GO-TermFinder-0.86-alt6_10.i586.rpm 0.86 i586 Autoimports
perl-GO-TermFinder - - -

Requires

Name Value
/usr/lib64/perl5 -
libc.so.6(GLIBC_2.2.5)(64bit) -
libc.so.6(GLIBC_2.3.4)(64bit) -
libc.so.6(GLIBC_2.4)(64bit) -
libgcc_s.so.1(GCC_3.0)(64bit) -
libm.so.6(GLIBC_2.2.5)(64bit) -
libperl-5.28.so()(64bit) -
libpthread.so.0(GLIBC_2.2.5)(64bit) -
libstdc++.so.6(CXXABI_1.3)(64bit) -
libstdc++.so.6(CXXABI_1.3.9)(64bit) -
libstdc++.so.6(GLIBCXX_3.4)(64bit) -
perl(CGI.pm) -
perl(DynaLoader.pm) -
perl(GD.pm) -
perl(GraphViz.pm) -
perl(IO/File.pm) -
perl(Storable.pm) -
perl(base.pm) -
perl(diagnostics.pm) -
rpmlib(PayloadIsLzma) -
rpmlib(SetVersions) -
rtld(GNU_HASH) -

Provides

Name Value
perl(GO/AnnotatedGene.pm) = 0.110
perl(GO/Annotation.pm) = 0.110
perl(GO/AnnotationProvider.pm) = 0.120
perl(GO/AnnotationProvider/AnnotationParser.pm) = 0.150
perl(GO/Node.pm) = 0.160
perl(GO/OntologyProvider.pm) = 0.120
perl(GO/OntologyProvider/OboParser.pm) = 0.010
perl(GO/OntologyProvider/OntologyParser.pm) = 0.150
perl(GO/Reference.pm) = 0.100
perl(GO/TermFinder.pm) = 0.860
perl(GO/TermFinder/Native.pm) -
perl(GO/TermFinderReport/Html.pm) = 0.120
perl(GO/TermFinderReport/Text.pm) = 0.100
perl(GO/Utils/File.pm) = 0.120
perl(GO/Utils/General.pm) = 0.110
perl(GO/View.pm) = 0.150
perl(GO/View/GD.pm) = 0.110
perl-GO-TermFinder = 0.86-alt6_10

Download

Type URL
Mirror ftp.altlinux.org
Binary Package perl-GO-TermFinder-0.86-alt6_10.x86_64.rpm
Source Package perl-GO-TermFinder-0.86-alt6_10.src.rpm

Install Howto

  1. Add the following line to /etc/apt/sources.list:
    
    rpm [Sisyphus] http://ftp.altlinux.org/pub/distributions/ALTLinux/autoimports/Sisyphus x86_64 autoimports
    rpm [Sisyphus] http://ftp.altlinux.org/pub/distributions/ALTLinux/autoimports/Sisyphus noarch autoimports
    
  2. Update the package index:
    # sudo apt-get update
  3. Install perl-GO-TermFinder rpm package:
    # sudo apt-get install perl-GO-TermFinder

Files

Path
/usr/lib64/perl5/GO/AnnotatedGene.pm
/usr/lib64/perl5/GO/Annotation.pm
/usr/lib64/perl5/GO/AnnotationProvider.pm
/usr/lib64/perl5/GO/Node.pm
/usr/lib64/perl5/GO/OntologyProvider.pm
/usr/lib64/perl5/GO/Reference.pm
/usr/lib64/perl5/GO/TermFinder.pm
/usr/lib64/perl5/GO/View.pm
/usr/lib64/perl5/GO/AnnotationProvider/AnnotationParser.pm
/usr/lib64/perl5/GO/OntologyProvider/OboParser.pm
/usr/lib64/perl5/GO/OntologyProvider/OntologyParser.pm
/usr/lib64/perl5/GO/TermFinder/Native.pm
/usr/lib64/perl5/GO/TermFinderReport/Html.pm
/usr/lib64/perl5/GO/TermFinderReport/Text.pm
/usr/lib64/perl5/GO/Utils/File.pm
/usr/lib64/perl5/GO/Utils/General.pm
/usr/lib64/perl5/GO/View/GD.pm
/usr/lib64/perl5/auto/GO-TermFinder
/usr/lib64/perl5/auto/GO/
/usr/lib64/perl5/auto/GO/TermFinder/
/usr/lib64/perl5/auto/GO/TermFinder/Native/Native.so
/usr/share/doc/perl-GO-TermFinder-0.86/Changes
/usr/share/doc/perl-GO-TermFinder-0.86/LICENSE
/usr/share/doc/perl-GO-TermFinder-0.86/README

See Also

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perl-GRID-Machine-0.127-alt4.1.x86_64.rpm Remote Procedure Calls over a SSH link
perl-GRID-Machine-scripts-0.127-alt4.1.x86_64.rpm GRID-Machine scripts
perl-GTop-0.18-alt10_27.x86_64.rpm Perl interface to libgtop
perl-Games-Cards-Poker-1.4-alt2.1.x86_64.rpm perl module Games-Cards-Poker
perl-Games-EternalLands-0.04-alt4.1.x86_64.rpm perl module Games-EternalLands
perl-Games-EternalLands-Binary-Float16-0.01-alt4.1.x86_64.rpm 16-bit floats as used by Eternal Lands
perl-Games-EternalLands-Binary-Unitvec16-0.01-alt4.1.x86_64.rpm 16-bit quantized unit vectors as used by Eternal Lands
perl-Games-Go-GMP-0.01-alt4.1.x86_64.rpm perl module Games-Go-GMP
perl-Games-Hack-Live-0.62-alt4.1.x86_64.rpm Perl script to ease playing games
perl-Games-Hack-Live-scripts-0.62-alt4.1.x86_64.rpm Games-Hack-Live scripts
perl-Games-RolePlay-MapGen-1.5008-alt5.1.x86_64.rpm The base object for generating dungeons and maps
perl-Gazelle-0.48-alt1.1.x86_64.rpm Preforked Plack Handler for performance freaks
perl-Geo-BUFR-1.37-alt1.x86_64.rpm Perl extension for handling of WMO BUFR files
perl-Geo-BUFR-scripts-1.37-alt1.x86_64.rpm Geo-BUFR scripts
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