Uses of Package
ubic.gemma.model.genome

Packages that use ubic.gemma.model.genome

Package	Description
ubic.gemma.cli.util
ubic.gemma.core.analysis.expression.coexpression.links
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.report
ubic.gemma.core.analysis.sequence
ubic.gemma.core.analysis.service
ubic.gemma.core.datastructure.matrix.io	This package contains I/O utilities for reading and writing expression data matrices.
ubic.gemma.core.goldenpath
ubic.gemma.core.loader.association
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.expression.geo
ubic.gemma.core.loader.genome
ubic.gemma.core.loader.genome.gene.ncbi
ubic.gemma.core.loader.genome.gene.ncbi.homology
ubic.gemma.core.loader.genome.taxon
ubic.gemma.core.loader.util.biomart
ubic.gemma.core.loader.util.mapper	Utilities for mapping Identifiable entities to external identifiers.
ubic.gemma.core.ontology
ubic.gemma.core.ontology.providers
ubic.gemma.core.search
ubic.gemma.core.search.source
ubic.gemma.core.visualization
ubic.gemma.core.visualization.cellbrowser	This package contains classes related to the Cell Browser visualization tool.
ubic.gemma.model.analysis.expression
ubic.gemma.model.analysis.expression.coexpression
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.association
ubic.gemma.model.association.coexpression
ubic.gemma.model.common.search
ubic.gemma.model.expression.arrayDesign
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.experiment
ubic.gemma.model.genome
ubic.gemma.model.genome.biosequence
ubic.gemma.model.genome.gene
ubic.gemma.model.genome.sequenceAnalysis
ubic.gemma.persistence.persister
ubic.gemma.persistence.service.analysis.expression.coexpression
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.association
ubic.gemma.persistence.service.association.coexpression
ubic.gemma.persistence.service.common.description
ubic.gemma.persistence.service.expression.arrayDesign
ubic.gemma.persistence.service.expression.bioAssayData
ubic.gemma.persistence.service.expression.designElement
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.service.genome
ubic.gemma.persistence.service.genome.biosequence
ubic.gemma.persistence.service.genome.gene
ubic.gemma.persistence.service.genome.sequenceAnalysis
ubic.gemma.persistence.service.genome.taxon
ubic.gemma.persistence.util
ubic.gemma.rest
ubic.gemma.rest.util.args
ubic.gemma.web.controller.expression.arrayDesign
ubic.gemma.web.controller.expression.experiment
ubic.gemma.web.controller.genome.gene

Classes in ubic.gemma.model.genome used by ubic.gemma.cli.util

Class	Description
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.core.analysis.expression.coexpression.links

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.core.analysis.expression.diff

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).

Classes in ubic.gemma.model.genome used by ubic.gemma.core.analysis.report

Class	Description
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.core.analysis.sequence

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
PhysicalLocation
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.core.analysis.service

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.core.datastructure.matrix.io

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).

Classes in ubic.gemma.model.genome used by ubic.gemma.core.goldenpath

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.core.loader.association

Class	Description
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.core.loader.expression.arrayDesign

Class	Description
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.core.loader.expression.geo

Class	Description
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.core.loader.genome

Class	Description
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.core.loader.genome.gene.ncbi

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.core.loader.genome.gene.ncbi.homology

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.core.loader.genome.taxon

Class	Description
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.core.loader.util.biomart

Class	Description
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.core.loader.util.mapper

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).

Classes in ubic.gemma.model.genome used by ubic.gemma.core.ontology

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.core.ontology.providers

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
GeneOntologyTermValueObject
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.core.search

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.core.search.source

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).

Classes in ubic.gemma.model.genome used by ubic.gemma.core.visualization

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).

Classes in ubic.gemma.model.genome used by ubic.gemma.core.visualization.cellbrowser

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).

Classes in ubic.gemma.model.genome used by ubic.gemma.model.analysis.expression

Class	Description
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.model.analysis.expression.coexpression

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).

Classes in ubic.gemma.model.genome used by ubic.gemma.model.analysis.expression.diff

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
TaxonValueObject

Classes in ubic.gemma.model.genome used by ubic.gemma.model.association

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).

Classes in ubic.gemma.model.genome used by ubic.gemma.model.association.coexpression

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).

Classes in ubic.gemma.model.genome used by ubic.gemma.model.common.search

Class	Description
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.model.expression.arrayDesign

Class	Description
Taxon
TaxonValueObject

Classes in ubic.gemma.model.genome used by ubic.gemma.model.expression.bioAssayData

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).

Classes in ubic.gemma.model.genome used by ubic.gemma.model.expression.biomaterial

Class	Description
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.model.expression.experiment

Class	Description
Taxon
TaxonValueObject

Classes in ubic.gemma.model.genome used by ubic.gemma.model.genome

Class	Description
Chromosome	Immutable representation of a chromosome
ChromosomeFeature	Some part of a chromosome
ChromosomeLocation
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
PhysicalLocation
Taxon
TaxonValueObject

Classes in ubic.gemma.model.genome used by ubic.gemma.model.genome.biosequence

Class	Description
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.model.genome.gene

Class	Description
ChromosomeFeature	Some part of a chromosome
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
PhysicalLocation
Taxon
TaxonValueObject

Classes in ubic.gemma.model.genome used by ubic.gemma.model.genome.sequenceAnalysis

Class	Description
Chromosome	Immutable representation of a chromosome
PhysicalLocation
TaxonValueObject

Classes in ubic.gemma.model.genome used by ubic.gemma.persistence.persister

Class	Description
Chromosome	Immutable representation of a chromosome
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.persistence.service.analysis.expression.coexpression

Class	Description
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.persistence.service.analysis.expression.diff

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.persistence.service.association

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.persistence.service.association.coexpression

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.persistence.service.common.description

Class	Description
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.persistence.service.expression.arrayDesign

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.persistence.service.expression.bioAssayData

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).

Classes in ubic.gemma.model.genome used by ubic.gemma.persistence.service.expression.designElement

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).

Classes in ubic.gemma.model.genome used by ubic.gemma.persistence.service.expression.experiment

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.persistence.service.genome

Class	Description
Chromosome	Immutable representation of a chromosome
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
PhysicalLocation
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.persistence.service.genome.biosequence

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).

Classes in ubic.gemma.model.genome used by ubic.gemma.persistence.service.genome.gene

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
PhysicalLocation
PhysicalLocationValueObject	A very simple value object to represent a physical location
Taxon
TaxonValueObject

Classes in ubic.gemma.model.genome used by ubic.gemma.persistence.service.genome.sequenceAnalysis

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).

Classes in ubic.gemma.model.genome used by ubic.gemma.persistence.service.genome.taxon

Class	Description
Taxon
TaxonValueObject

Classes in ubic.gemma.model.genome used by ubic.gemma.persistence.util

Class	Description
Chromosome	Immutable representation of a chromosome
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
PhysicalLocation
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.rest

Class	Description
GeneOntologyTermValueObject
PhysicalLocationValueObject	A very simple value object to represent a physical location
Taxon
TaxonValueObject

Classes in ubic.gemma.model.genome used by ubic.gemma.rest.util.args

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
GeneOntologyTermValueObject
PhysicalLocationValueObject	A very simple value object to represent a physical location
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.web.controller.expression.arrayDesign

Class	Description
Taxon

Classes in ubic.gemma.model.genome used by ubic.gemma.web.controller.expression.experiment

Class	Description
Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).

Classes in ubic.gemma.model.genome used by ubic.gemma.web.controller.genome.gene

Class	Description
TaxonValueObject