Gemma Core 1.32.0-SNAPSHOT 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.convert	Convert data from one QuantitationType to another.
ubic.gemma.core.analysis.preprocess.detect	This package contains classes for detecting and linting expression data.
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.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
ubic.gemma.core.datastructure.matrix	This package contains data structures for representing matrices of gene expression.
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.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.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.singleCell	This package contains specific logic for dealing with single-cell data from GEO.
ubic.gemma.core.loader.expression.geo.util
ubic.gemma.core.loader.expression.simple
ubic.gemma.core.loader.expression.simple.model
ubic.gemma.core.loader.expression.singleCell	This package contains classes for loading single cell expression data.
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.anndata
ubic.gemma.core.loader.util.biomart
ubic.gemma.core.loader.util.converter
ubic.gemma.core.loader.util.fetcher
ubic.gemma.core.loader.util.ftp	Utilities for working with FTP.
ubic.gemma.core.loader.util.hdf5	Minimalistic read-only wrapper around HDF5 native library.
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.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.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.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.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