GO - Gene Ontology Simple Utility Class River stage zero No dependents

This is a simple interface to the GO toolkit TIP FOR PROGRAMMERS: If you are already familiar with object oriented perl, you should use the GO::AppHandle class; this module is intended as a simple convenience wrapper for a small section of the perl A...

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

Sub::Go - DWIM sub blocks for smart matching River stage zero No dependents

In case you don't know, smart matching ("~~") data against a code block will run the block once (for scalars) or, distributively, many times for arrays and hashes: [1..10] ~~ sub { say shift }; @arr ~~ sub { say shift }; %h ~~ sub { ... }; The motiva...

RODRIGO/Sub-Go-0.01 - 11 Jul 2011 09:05:54 GMT

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 GMT

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 GMT

GO::Basic - basic procedural interface to go-perl River stage one • 1 direct dependent • 1 total dependent

CMUNGALL/go-perl-0.15 - 12 Jun 2013 16:22:41 GMT

GO::Tango - Tango ANnotates GO River stage zero No dependents

THIS IS ALPHA CODE; API SUBJECT TO CHANGE...

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

GO::Parser - parses all GO files formats and types River stage one • 1 direct dependent • 1 total dependent

Module for parsing GO flat files; for examples of GO/OBO flatfile formats see: <ftp://ftp.geneontology.org/pub/go/ontology> <ftp://ftp.geneontology.org/pub/go/gene-associations> For a description of the various file formats, see: <http://www.geneonto...

CMUNGALL/go-perl-0.15 - 12 Jun 2013 16:22:41 GMT

GO::Reference River stage zero No dependents

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

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 GMT

GO::DebugUtils River stage zero No dependents

Miscellaneous debugging utilities...

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

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 GMT

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 GMT

GO::SqlWrapper River stage zero No dependents

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

GO::ObjFactory - GO Object Factory River stage one • 1 direct dependent • 1 total dependent

You only need to be aware of this class if you are generating new objects. You should not directly create objects like this: $term = GO::Model::Term->new($h); Instead you should create them like this: $fac = GO::ObjFactory->new(); $term = $fac->creat...

CMUNGALL/go-perl-0.15 - 12 Jun 2013 16:22:41 GMT

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 GMT

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 GMT

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 GMT

GO/Admin.pm River stage zero No dependents

object to help administer GO dbs use the script go-dev/scripts/go-manager.pl...

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

GO/Utils.pm River stage one • 1 direct dependent • 1 total dependent

CMUNGALL/go-perl-0.15 - 12 Jun 2013 16:22:41 GMT

GO/ObjCache.pm River stage one • 1 direct dependent • 1 total dependent

This is a kind of GO::ObjFactory - you should not need to use this method directly...

CMUNGALL/go-perl-0.15 - 12 Jun 2013 16:22:41 GMT

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