Gemma Core 1.31.5 API

Packages

Package	Description
ubic.gemma.core.analysis.expression
ubic.gemma.core.analysis.expression.coexpression
ubic.gemma.core.analysis.expression.coexpression.links
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess
ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.analysis.preprocess.filter
ubic.gemma.core.analysis.preprocess.normalize
ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.analysis.report
ubic.gemma.core.analysis.sequence
ubic.gemma.core.analysis.service
ubic.gemma.core.analysis.util
ubic.gemma.core.annotation.reference
ubic.gemma.core.apps
ubic.gemma.core.association.phenotype
ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence
ubic.gemma.core.datastructure.matrix
ubic.gemma.core.expression.experiment
ubic.gemma.core.expression.experiment.service
ubic.gemma.core.externalDb
ubic.gemma.core.genome.gene
ubic.gemma.core.genome.gene.service
ubic.gemma.core.image
ubic.gemma.core.image.aba
ubic.gemma.core.job
ubic.gemma.core.job.executor.common
ubic.gemma.core.job.executor.webapp
ubic.gemma.core.job.progress
ubic.gemma.core.loader.association
ubic.gemma.core.loader.association.phenotype
ubic.gemma.core.loader.entrez
ubic.gemma.core.loader.entrez.pubmed
ubic.gemma.core.loader.expression
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.expression.arrayExpress
ubic.gemma.core.loader.expression.arrayExpress.util
ubic.gemma.core.loader.expression.geo
ubic.gemma.core.loader.expression.geo.fetcher
ubic.gemma.core.loader.expression.geo.model
ubic.gemma.core.loader.expression.geo.service
ubic.gemma.core.loader.expression.geo.util
ubic.gemma.core.loader.expression.simple
ubic.gemma.core.loader.expression.simple.model
ubic.gemma.core.loader.genome
ubic.gemma.core.loader.genome.gene
ubic.gemma.core.loader.genome.gene.ncbi
ubic.gemma.core.loader.genome.gene.ncbi.homology
ubic.gemma.core.loader.genome.gene.ncbi.model
ubic.gemma.core.loader.genome.taxon
ubic.gemma.core.loader.util
ubic.gemma.core.loader.util.biomart
ubic.gemma.core.loader.util.converter
ubic.gemma.core.loader.util.fetcher
ubic.gemma.core.loader.util.parser
ubic.gemma.core.loader.util.sdo
ubic.gemma.core.metrics
ubic.gemma.core.metrics.binder
ubic.gemma.core.metrics.binder.cache
ubic.gemma.core.metrics.binder.database
ubic.gemma.core.metrics.binder.jpa
ubic.gemma.core.ontology
ubic.gemma.core.ontology.jena	This package contains all the Jena-related code for ontologies that Gemma needs.
ubic.gemma.core.ontology.providers
ubic.gemma.core.search
ubic.gemma.core.search.lucene
ubic.gemma.core.search.source
ubic.gemma.core.security.audit
ubic.gemma.core.security.authentication
ubic.gemma.core.security.authorization.acl
ubic.gemma.core.tasks
ubic.gemma.core.tasks.analysis.coexp
ubic.gemma.core.tasks.analysis.diffex
ubic.gemma.core.tasks.analysis.expression
ubic.gemma.core.tasks.analysis.sequence
ubic.gemma.core.tasks.maintenance
ubic.gemma.core.tasks.visualization
ubic.gemma.core.util
ubic.gemma.core.util.concurrent
ubic.gemma.core.visualization
ubic.gemma.model
ubic.gemma.model.analysis
ubic.gemma.model.analysis.expression
ubic.gemma.model.analysis.expression.coexpression
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.analysis.expression.pca
ubic.gemma.model.annotations
ubic.gemma.model.association
ubic.gemma.model.association.coexpression
ubic.gemma.model.association.phenotype
ubic.gemma.model.common
ubic.gemma.model.common.auditAndSecurity
ubic.gemma.model.common.auditAndSecurity.curation
ubic.gemma.model.common.auditAndSecurity.eventType
ubic.gemma.model.common.description
ubic.gemma.model.common.measurement
ubic.gemma.model.common.protocol
ubic.gemma.model.common.quantitationtype
ubic.gemma.model.common.search
ubic.gemma.model.expression
ubic.gemma.model.expression.arrayDesign
ubic.gemma.model.expression.bioAssay
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.designElement
ubic.gemma.model.expression.experiment
ubic.gemma.model.genome
ubic.gemma.model.genome.biosequence
ubic.gemma.model.genome.gene
ubic.gemma.model.genome.gene.phenotype
ubic.gemma.model.genome.gene.phenotype.valueObject
ubic.gemma.model.genome.sequenceAnalysis
ubic.gemma.persistence.cache
ubic.gemma.persistence.hibernate
ubic.gemma.persistence.model
ubic.gemma.persistence.persister
ubic.gemma.persistence.retry
ubic.gemma.persistence.service
ubic.gemma.persistence.service.analysis
ubic.gemma.persistence.service.analysis.expression
ubic.gemma.persistence.service.analysis.expression.coexpression
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.analysis.expression.pca
ubic.gemma.persistence.service.analysis.expression.sampleCoexpression
ubic.gemma.persistence.service.association
ubic.gemma.persistence.service.association.coexpression
ubic.gemma.persistence.service.association.phenotype
ubic.gemma.persistence.service.association.phenotype.service
ubic.gemma.persistence.service.common
ubic.gemma.persistence.service.common.auditAndSecurity
ubic.gemma.persistence.service.common.auditAndSecurity.curation
ubic.gemma.persistence.service.common.description
ubic.gemma.persistence.service.common.measurement
ubic.gemma.persistence.service.common.protocol
ubic.gemma.persistence.service.common.quantitationtype
ubic.gemma.persistence.service.expression.arrayDesign
ubic.gemma.persistence.service.expression.bioAssay
ubic.gemma.persistence.service.expression.bioAssayData
ubic.gemma.persistence.service.expression.biomaterial
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