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GO-TermFinder-0.71
River stage zero No dependents

Changes for version 0.71

  • native/Makefile.PL
  • Fix for the compilation of the C++ code that carries out the math. It is now hard-coded to use g++ as the LD and CC variables, and will complain if it can't find g++. If it fails, it will tell you what needs editing to hopefully fix it.
  • GO::TermFinder
  • Small amount of refactoring on the findTerms() method, to make it easier to follow. This doesn't change the functionality.
  • Added logic such that if a background population is provided, but then the list of genes for which enriched terms are to be found has genes not in that background population, then those genes are discarded from the calculation, and a new method, discardedGenes, allows the identify of those genes to be determined.
  • tests
  • Added some new tests, and make sure all code uses strict and warnings

Modules

GO::AnnotatedGene
GO::Annotation
GO::AnnotationProvider
abstract base class defining interface for how Annotation information should be provided
GO::AnnotationProvider::AnnotationParser
parses a gene annotation file
GO::Node
provides information about a node in the Gene Ontology
GO::OntologyProvider
abstract base class providing API for the provision on Gene Ontology information
GO::OntologyProvider::OntologyParser
Provides API for retrieving data from Gene Ontology files
GO::Reference
GO::TermFinder
identify GO nodes that annotate a group of genes with a significant p-value
GO::TermFinderReport::Html
prints an html table of the results of GO::TermFinder
GO::TermFinderReport::Text
prints results of GO::TermFinder as a text report
GO::Utils::File
simply utility module for dealing with file parsing
GO::Utils::General
provides some general utilities for clients of other GO classes
GO::View
Creates a gif or png image for visualizing the GO DAG
GO::View::GD
a helper class for GO::View to deal with the image

Provides

GO::TermFinder::Native
in lib/GO/TermFinder/Native.pm
GO::TermFinder::Native::Distributions
in lib/GO/TermFinder/Native.pm
GO::TermFinder::Nativec
in lib/GO/TermFinder/Native.pm

Examples

Other files