Gemma 1.32.0-SNAPSHOT API

Packages 
Package Description
ubic.gemma.apps
This package contains built-in Gemma CLI applications.
ubic.gemma.cli.authentication  
ubic.gemma.cli.batch
Utilities for executing batch jobs via the CLI.
ubic.gemma.cli.completion
This package provides completion support for the Gemma CLI.
ubic.gemma.cli.config  
ubic.gemma.cli.logging  
ubic.gemma.cli.logging.log4j  
ubic.gemma.cli.main  
ubic.gemma.cli.metrics  
ubic.gemma.cli.util  
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
This package contains classes for preprocessing expression data.
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.slice
This package provides capabilities for slicing BulkExpressionDataVector.
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.singleCell
This package contains classes for analysing single-cell expression data.
ubic.gemma.core.analysis.singleCell.aggregate
This packge contains classes for splitting and aggregating single-cell data.
ubic.gemma.core.analysis.stats
This package contains classes for computing various statistics.
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
This package contains interfaces and classes for loading expression data.
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.fetcher2
Provides classes for fetching data from various sources.
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.sequencing
This package contains interfaces and classes for loading sequencing data.
ubic.gemma.core.loader.expression.simple  
ubic.gemma.core.loader.expression.simple.model
Model classes for loading simple expression data.
ubic.gemma.core.loader.expression.singleCell
This package contains classes for loading single cell expression data.
ubic.gemma.core.loader.expression.singleCell.metadata
This package contains classes for loading single-cell metadata such as cell type assignment and cell-level characteristics.
ubic.gemma.core.loader.expression.singleCell.transform
This package contains classes for transforming 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.fetcher2
Provides classes for fetching data from various sources.
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.mapper
Utilities for mapping Identifiable entities to external identifiers.
ubic.gemma.core.loader.util.parser  
ubic.gemma.core.loader.util.sdo  
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 gemma.gsec.authentication.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.util.locking
Utilities for locking files.
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.model.util  
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  
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.context  
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.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.scheduler.jobs
This packages contains Quartz job definitions.
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