Uses of Package
ubic.erminej.data

Packages that use ubic.erminej.data

Package	Description
ubic.erminej
ubic.erminej.analysis
ubic.erminej.data
ubic.erminej.gui
ubic.erminej.gui.analysis
ubic.erminej.gui.geneset
ubic.erminej.gui.geneset.details
ubic.erminej.gui.geneset.edit
ubic.erminej.gui.geneset.table
ubic.erminej.gui.geneset.tree
ubic.erminej.gui.table
ubic.erminej.gui.util

Classes in ubic.erminej.data used by ubic.erminej

Class and Description
GeneAnnotationParser.Format
GeneAnnotations Maintains gene annotations.
GeneSetTerm Represents a GO term (most commonly) or other way of grouping genes.
GeneSetTerms Maintain information on GeneSetTerms (including but not limited GO terms).

Classes in ubic.erminej.data used by ubic.erminej.analysis

Class and Description
Gene Represents a Gene entity.
GeneAnnotations Maintains gene annotations.
GeneScores Parse and store probe->score associations.
GeneSetResult Data structure to store class scoring information about a class.
GeneSetTerm Represents a GO term (most commonly) or other way of grouping genes.
Histogram Stores distributions for geneSets ( a series of histograms).
Probe Represents an assayable item such as a microarray probe (or probeset) that can refer to more than one gene.

Classes in ubic.erminej.data used by ubic.erminej.data

Class and Description
Gene Represents a Gene entity.
GeneAnnotationParser.Format
GeneAnnotations Maintains gene annotations.
GeneScores Parse and store probe->score associations.
GeneSet A group of genes, such as those defined by GO annotations or KEGG pathways.
GeneSetDetails Combination of scores and data for a gene set, for visualization
GeneSetResult Data structure to store class scoring information about a class.
GeneSetTerm Represents a GO term (most commonly) or other way of grouping genes.
GeneSetTerms Maintain information on GeneSetTerms (including but not limited GO terms).
Multifunctionality Implementation of multifunctionality computations as described in Gillis and Pavlidis (2011) PLoS ONE 6:2:e17258.
Probe Represents an assayable item such as a microarray probe (or probeset) that can refer to more than one gene.
UserDefinedGeneSetManager.GeneSetFileFormat

Classes in ubic.erminej.data used by ubic.erminej.gui

Class and Description
GeneAnnotations Maintains gene annotations.
GeneSet A group of genes, such as those defined by GO annotations or KEGG pathways.
GeneSetTerm Represents a GO term (most commonly) or other way of grouping genes.
Histogram Stores distributions for geneSets ( a series of histograms).

Classes in ubic.erminej.data used by ubic.erminej.gui.analysis

Class and Description
GeneAnnotations Maintains gene annotations.

Classes in ubic.erminej.data used by ubic.erminej.gui.geneset

Class and Description
GeneAnnotations Maintains gene annotations.
GeneSet A group of genes, such as those defined by GO annotations or KEGG pathways.
GeneSetTerm Represents a GO term (most commonly) or other way of grouping genes.
Probe Represents an assayable item such as a microarray probe (or probeset) that can refer to more than one gene.

Classes in ubic.erminej.data used by ubic.erminej.gui.geneset.details

Class and Description
GeneSetDetails Combination of scores and data for a gene set, for visualization
Probe Represents an assayable item such as a microarray probe (or probeset) that can refer to more than one gene.

Classes in ubic.erminej.data used by ubic.erminej.gui.geneset.edit

Class and Description
Gene Represents a Gene entity.
GeneAnnotations Maintains gene annotations.
GeneSet A group of genes, such as those defined by GO annotations or KEGG pathways.
GeneSetTerm Represents a GO term (most commonly) or other way of grouping genes.
Probe Represents an assayable item such as a microarray probe (or probeset) that can refer to more than one gene.

Classes in ubic.erminej.data used by ubic.erminej.gui.geneset.table

Class and Description
GeneAnnotations Maintains gene annotations.
GeneSetTerm Represents a GO term (most commonly) or other way of grouping genes.

Classes in ubic.erminej.data used by ubic.erminej.gui.geneset.tree

Class and Description
GeneAnnotations Maintains gene annotations.
GeneSetTerm Represents a GO term (most commonly) or other way of grouping genes.

Classes in ubic.erminej.data used by ubic.erminej.gui.table

Class and Description
Probe Represents an assayable item such as a microarray probe (or probeset) that can refer to more than one gene.

Classes in ubic.erminej.data used by ubic.erminej.gui.util

Class and Description
GeneSetResult Data structure to store class scoring information about a class.