perl-Bio-FdrFet - Perl extension for False Discovery Rate and Fisher Exact Test applied to pathway analysis

Property Value
Distribution ALT Linux Sisyphus
Repository Autoimports noarch
Package name perl-Bio-FdrFet
Package version 0.05
Package release alt1
Package architecture noarch
Package type rpm
Installed size 32.53 KB
Download size 32.53 KB
Official Mirror
Bio::FdrFet implements the False Discovery Rate Fisher Exact Test of gene.expression analysis applied to pathways described in the paper by
Ruiru Ji, Karl-Heinz Ott, Roumyana Yordanova, and Robert E
Bruccoleri.  A copy of the paper is included with the distribution in
the file, Fdr-Fet-Manuscript.pdf.
The module is implemented using a simple object oriented paradigm
where the object stores all the information needed for a calculation
along with a state variable, `STATE'. The state variable has two
possible values, `'setup'' and `'calculated''. The value of
`'setup'' indicates that the object is being setup with data, and any
results in the object are inconsistent with the data. The value of
`'calculated'' indicates that the object's computational results are
consistent with the data, and may be returned to a calling program.
The `'calculate'' method is used to update all the calculated values
from the input data. It checks the state variable first, and only does
the calculation if the state is `'setup''. Once the calculations are
complete, then the state variable is set to `'calculated''. Thus, the `calculate' method
can be called whenever a calculated value is needed, and there is no
performance penalty.
The module initializes the `Bio::FdrFet' object with a state of
`'setup''. Any data input sets the state to `'setup''. Any requests
for calculated data, calls `'calculate'', which updates the state
variable so futures requests for calculated data return quickly.


Package Version Architecture Repository
perl-Bio-FdrFet - - -


Name Value
/usr/bin/perl -
/usr/share/perl5 -
perl(Getopt/ -
perl( >= 0.450
rpmlib(PayloadIsLzma) -


Name Value
perl(Bio/ = 0.050
perl(Bio/ -
perl-Bio-FdrFet = 0.05-alt1


Type URL
Binary Package perl-Bio-FdrFet-0.05-alt1.noarch.rpm
Source Package perl-Bio-FdrFet-0.05-alt1.src.rpm

Install Howto

  1. Add the following line to /etc/apt/sources.list:
    rpm [Sisyphus] noarch autoimports
    rpm [Sisyphus] noarch autoimports
  2. Update the package index:
    # sudo apt-get update
  3. Install perl-Bio-FdrFet rpm package:
    # sudo apt-get install perl-Bio-FdrFet



See Also

Package Description
perl-Bio-FdrFet-scripts-0.05-alt1.noarch.rpm Bio-FdrFet scripts
perl-Bio-GFF3-2.0-alt1.noarch.rpm fast, low-level GFF3 manipulation
perl-Bio-GFF3-scripts-2.0-alt1.noarch.rpm Bio-GFF3 scripts
perl-Bio-GMOD-Blast-Graph-0.06-alt1.noarch.rpm display a graphical summary of a BLAST report
perl-Bio-GenBankParser-0.05-alt1.noarch.rpm Parse::RecDescent parser for a GenBank record
perl-Bio-Glite-0.10-alt1.noarch.rpm G-language Genome Analysis Environment REST service interface module
perl-Bio-Graphics-2.25-alt1_6.noarch.rpm Generate GD images of Bio::Seq objects
perl-Bio-Graphics-Glyph-decorated_gene-0.03-alt1.noarch.rpm perl module Bio-Graphics-Glyph-decorated_gene
perl-Bio-Grep-0.10.6-alt1.noarch.rpm Perl extension for searching in DNA and Protein sequences
perl-Bio-Grep-scripts-0.10.6-alt1.noarch.rpm Bio-Grep scripts
perl-Bio-IlluminaSAV-1.0.9706-alt2.noarch.rpm Bio::IlluminaSAV - Parse Illumina SAV files
perl-Bio-JBrowse-Store-NCList-0.1-alt1.noarch.rpm modules for formatting JSON nested containment lists for use with JBrowse
perl-Bio-KEGGI-0.1.50-alt1.noarch.rpm Module to handle KEGG genome, ko and pathway files
perl-Bio-Kmer-0.21-alt1.noarch.rpm >new("file.fastq.gz",{kmercounter=>"jellyfish",numcpus=>4});
perl-Bio-LITE-Taxonomy-0.07-alt1.noarch.rpm Lightweight and efficient taxonomic tree manager