Gemma 1.31.13-SNAPSHOT API

Packages

Package	Description
ubic.gemma.contrib.apps	This package can be used by other Java packages to include CLIs.
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.apps
ubic.gemma.core.association.phenotype
ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence
ubic.gemma.core.completion	This package provides completion support for the Gemma CLI.
ubic.gemma.core.config	This package contains classes that are used to manage Gemma's Spring context.
ubic.gemma.core.context	This package contains classes that are used to manage Gemma's Spring context.
ubic.gemma.core.datastructure.matrix
ubic.gemma.core.goldenpath
ubic.gemma.core.image
ubic.gemma.core.image.aba
ubic.gemma.core.job	Provides functionalities for running background tasks.
ubic.gemma.core.job.notification
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.logging
ubic.gemma.core.logging.log4j
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.profiling	Classes and utilities for profiling the performance of Gemma.
ubic.gemma.core.search
ubic.gemma.core.search.lucene
ubic.gemma.core.search.source
ubic.gemma.core.security
ubic.gemma.core.security.audit
ubic.gemma.core.security.authentication	This package contains implementation of gsec UserService and UserManager.
ubic.gemma.core.security.authorization.acl
ubic.gemma.core.tasks	This package contains task definitions.
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.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.blacklist
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.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	This package contains classes related to retrieval and persistence of entities.
ubic.gemma.persistence.cache
ubic.gemma.persistence.hibernate	This package contains Hibernate-related classes and utilities for persisting entities.
ubic.gemma.persistence.initialization
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.blacklist	Service for managing blacklisted entities.
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.service.maintenance	Contains classes related to database maintenance.
ubic.gemma.persistence.util
ubic.gemma.rest
ubic.gemma.rest.analytics
ubic.gemma.rest.analytics.ga4
ubic.gemma.rest.annotations
ubic.gemma.rest.providers
ubic.gemma.rest.security
ubic.gemma.rest.serializers
ubic.gemma.rest.servlet
ubic.gemma.rest.swagger.resolver
ubic.gemma.rest.util
ubic.gemma.rest.util.args
ubic.gemma.web.controller
ubic.gemma.web.controller.analysis.expression.coexpression.links
ubic.gemma.web.controller.analysis.preprocess
ubic.gemma.web.controller.analysis.sequence
ubic.gemma.web.controller.coexpressionSearch
ubic.gemma.web.controller.common
ubic.gemma.web.controller.common.auditAndSecurity
ubic.gemma.web.controller.common.auditAndSecurity.recaptcha
ubic.gemma.web.controller.common.description.bibref
ubic.gemma.web.controller.common.rss
ubic.gemma.web.controller.diff
ubic.gemma.web.controller.expression.arrayDesign
ubic.gemma.web.controller.expression.bioAssay
ubic.gemma.web.controller.expression.biomaterial
ubic.gemma.web.controller.expression.designElement
ubic.gemma.web.controller.expression.experiment
ubic.gemma.web.controller.genome
ubic.gemma.web.controller.genome.gene
ubic.gemma.web.controller.monitoring
ubic.gemma.web.controller.visualization
ubic.gemma.web.feed
ubic.gemma.web.job.progress
ubic.gemma.web.listener
ubic.gemma.web.logging
ubic.gemma.web.metrics
ubic.gemma.web.metrics.binder.servlet
ubic.gemma.web.persistence
ubic.gemma.web.propertyeditor
ubic.gemma.web.remote
ubic.gemma.web.scheduler
ubic.gemma.web.services
ubic.gemma.web.taglib
ubic.gemma.web.taglib.arrayDesign
ubic.gemma.web.taglib.common.auditAndSecurity
ubic.gemma.web.taglib.expression.experiment
ubic.gemma.web.tasks.analysis.sequence
ubic.gemma.web.util
ubic.gemma.web.util.upload
ubic.gemma.web.view