GO::TermFinder - identify GO nodes that annotate a group of genes with a significant p-value River stage zero No dependents

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 gen...

SHERLOCK/GO-TermFinder-0.86 - 19 Nov 2009 17:39:14 UTC

lib/GO/TermFinder/Native.pm River stage zero No dependents

SHERLOCK/GO-TermFinder-0.86 - 19 Nov 2009 17:39:14 UTC

GO::Node - provides information about a node in the Gene Ontology River stage zero No dependents

The GO::Node package is intended to be used as a container for information about a node in one of the three Gene Ontologies. It allows the storage of the goid, and immediate parents and children, as well as paths to the top of the ontology. This pack...

SHERLOCK/GO-TermFinder-0.86 - 19 Nov 2009 17:39:14 UTC

GO::View - Creates a gif or png image for visualizing the GO DAG River stage zero No dependents

This perl module generates a graphic that displays the parent and child relationships of a selected GO term. It also provides the visualization for the GO::TermFinder perl module created by the Stanford Microarray Database (SMD). This module is usefu...

SHERLOCK/GO-TermFinder-0.86 - 19 Nov 2009 17:39:14 UTC

GO::Reference River stage zero No dependents

SHERLOCK/GO-TermFinder-0.86 - 19 Nov 2009 17:39:14 UTC

GO::Annotation River stage zero No dependents

This package currently does nothing, but is a placeholder for future development.......

SHERLOCK/GO-TermFinder-0.86 - 19 Nov 2009 17:39:14 UTC

GO::AnnotatedGene River stage zero No dependents

The GO::AnnotatedGene package allows creation of objects that contains the details of a gene as determined from a gene_associations file. Typically these objects will contain the following information: Column Cardinality Contents ------ ----------- -...

SHERLOCK/GO-TermFinder-0.86 - 19 Nov 2009 17:39:14 UTC

GO::OntologyProvider - abstract base class providing API for the provision on Gene Ontology information River stage zero No dependents

GO::OntologyProvider is an abstract class that defines an interface that should be implemented by specific subclasses, which may read ontology information from databases, flatfiles, XML files etc. All of the methods return either one or many GO::Node...

SHERLOCK/GO-TermFinder-0.86 - 19 Nov 2009 17:39:14 UTC

GO::AnnotationProvider - abstract base class defining interface for how Annotation information should be provided River stage zero No dependents

GO::AnnotationProvider is an interface that defines an API that should be implemented by specific subclasses, which may read GO annotation from databases, flatfiles, XML files etc. GO (Gene Ontology) is a project of the Gene Ontology Consortium (http...

SHERLOCK/GO-TermFinder-0.86 - 19 Nov 2009 17:39:14 UTC

GO::View::GD - a helper class for GO::View to deal with the image River stage zero No dependents

SHERLOCK/GO-TermFinder-0.86 - 19 Nov 2009 17:39:14 UTC

GO::Utils::File - simply utility module for dealing with file parsing River stage zero No dependents

SHERLOCK/GO-TermFinder-0.86 - 19 Nov 2009 17:39:14 UTC

GO::Utils::General - provides some general utilities for clients of other GO classes River stage zero No dependents

SHERLOCK/GO-TermFinder-0.86 - 19 Nov 2009 17:39:14 UTC

GO::TermFinderReport::Text - prints results of GO::TermFinder as a text report River stage zero No dependents

This print() method of this Perl module receives a reference to an the array that is the return value from the findTerms method of GO::TermFinder, the number of genes that were used to generate the terms, and the number of genes that were said to be ...

SHERLOCK/GO-TermFinder-0.86 - 19 Nov 2009 17:39:14 UTC

GO::TermFinderReport::Html - prints an html table of the results of GO::TermFinder River stage zero No dependents

This print() method of this Perl module receives a reference to an the array that is the return value from the findTerms method of GO::TermFinder, the aspect for which terms were found, the number of genes that were used to generate the terms, and th...

SHERLOCK/GO-TermFinder-0.86 - 19 Nov 2009 17:39:14 UTC

GO::OntologyProvider::OboParser - Provides API for retrieving data from Gene Ontology obo file. River stage zero No dependents

GO::OntologyProvider::OboParser implements the interface defined by GO::OntologyProvider, and parses the gene ontology obo file (GO) in plain text (not XML) format. These files can be obtained from the Gene Ontology Consortium web site, http://www.ge...

SHERLOCK/GO-TermFinder-0.86 - 19 Nov 2009 17:39:14 UTC

GO::OntologyProvider::OntologyParser - Provides API for retrieving data from Gene Ontology files River stage zero No dependents

GO::OntologyProvider::OntologyParser implements the interface defined by GO::OntologyProvider, and parses a gene ontology file (GO) in plain text (not XML) format. These files can be obtained from the Gene Ontology Consortium web site, http://www.gen...

SHERLOCK/GO-TermFinder-0.86 - 19 Nov 2009 17:39:14 UTC

GO::AnnotationProvider::AnnotationParser - parses a gene annotation file River stage zero No dependents

GO::AnnotationProvider::AnnotationParser is a concrete subclass of GO::AnnotationProvider, and creates a data structure mapping gene names to GO annotations by parsing a file of annotations provided by the Gene Ontology Consortium. This package provi...

SHERLOCK/GO-TermFinder-0.86 - 19 Nov 2009 17:39:14 UTC

GO::AppHandle - Gene Ontology Data API handle River stage zero No dependents

This is a module for accessing Gene Ontology data sources, e.g the GO relational database. It defines a set of methods that provide a consistent interface independent of the way the GO data is stored. For an explanation of the GO project, please visi...

SJCARBON/go-db-perl-0.04 - 21 Dec 2009 21:56:44 UTC
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