| ubic.gemma.core.analysis.expression |
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| ubic.gemma.core.analysis.expression.coexpression |
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| ubic.gemma.core.analysis.expression.coexpression.links |
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| ubic.gemma.core.analysis.expression.diff |
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| ubic.gemma.core.analysis.preprocess |
This package contains classes for preprocessing expression data.
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| ubic.gemma.core.analysis.preprocess.batcheffects |
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| ubic.gemma.core.analysis.preprocess.convert |
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| ubic.gemma.core.analysis.preprocess.detect |
This package contains classes for detecting and linting expression data.
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| ubic.gemma.core.analysis.preprocess.filter |
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| ubic.gemma.core.analysis.preprocess.normalize |
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| ubic.gemma.core.analysis.preprocess.slice |
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| ubic.gemma.core.analysis.preprocess.svd |
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| ubic.gemma.core.analysis.report |
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| ubic.gemma.core.analysis.sequence |
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| ubic.gemma.core.analysis.service |
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| ubic.gemma.core.analysis.singleCell |
This package contains classes for analysing single-cell expression data.
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| ubic.gemma.core.analysis.singleCell.aggregate |
This packge contains classes for splitting and aggregating single-cell data.
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| ubic.gemma.core.analysis.stats |
This package contains classes for computing various statistics.
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| ubic.gemma.core.config |
This package contains classes that are used to manage Gemma's Spring context.
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| ubic.gemma.core.context |
This package contains classes that are used to manage Gemma's Spring context.
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| ubic.gemma.core.datastructure |
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| ubic.gemma.core.datastructure.matrix |
This package contains data structures for representing matrices of gene expression.
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| ubic.gemma.core.datastructure.matrix.io |
This package contains I/O utilities for reading and writing expression data matrices.
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| ubic.gemma.core.goldenpath |
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| ubic.gemma.core.job |
Provides functionalities for running background tasks.
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| ubic.gemma.core.job.notification |
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| ubic.gemma.core.job.progress |
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| ubic.gemma.core.loader.association |
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| ubic.gemma.core.loader.entrez |
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| ubic.gemma.core.loader.entrez.pubmed |
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| ubic.gemma.core.loader.expression |
This package contains interfaces and classes for loading expression data.
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| ubic.gemma.core.loader.expression.arrayDesign |
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| ubic.gemma.core.loader.expression.arrayExpress |
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| ubic.gemma.core.loader.expression.arrayExpress.util |
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| ubic.gemma.core.loader.expression.geo |
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| ubic.gemma.core.loader.expression.geo.fetcher |
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| ubic.gemma.core.loader.expression.geo.fetcher2 |
Provides classes for fetching data from various sources.
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| ubic.gemma.core.loader.expression.geo.model |
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| ubic.gemma.core.loader.expression.geo.service |
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| ubic.gemma.core.loader.expression.geo.singleCell |
This package contains specific logic for dealing with single-cell data from GEO.
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| ubic.gemma.core.loader.expression.geo.util |
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| ubic.gemma.core.loader.expression.sequencing |
This package contains interfaces and classes for loading sequencing data.
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| ubic.gemma.core.loader.expression.simple |
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| ubic.gemma.core.loader.expression.simple.model |
Model classes for loading simple expression data.
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| ubic.gemma.core.loader.expression.singleCell |
This package contains classes for loading single cell expression data.
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| 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.
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| ubic.gemma.core.loader.expression.singleCell.transform |
This package contains classes for transforming single cell expression data.
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| ubic.gemma.core.loader.genome |
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| ubic.gemma.core.loader.genome.gene |
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| ubic.gemma.core.loader.genome.gene.ncbi |
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| ubic.gemma.core.loader.genome.gene.ncbi.homology |
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| ubic.gemma.core.loader.genome.gene.ncbi.model |
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| ubic.gemma.core.loader.genome.taxon |
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| ubic.gemma.core.loader.util |
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| ubic.gemma.core.loader.util.anndata |
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| ubic.gemma.core.loader.util.biomart |
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| ubic.gemma.core.loader.util.converter |
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| ubic.gemma.core.loader.util.fetcher |
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| ubic.gemma.core.loader.util.fetcher2 |
Provides classes for fetching data from various sources.
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| ubic.gemma.core.loader.util.ftp |
Utilities for working with FTP.
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| ubic.gemma.core.loader.util.hdf5 |
Minimalistic read-only wrapper around HDF5 native library.
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| ubic.gemma.core.loader.util.mapper |
Utilities for mapping Identifiable entities to external identifiers. |
| ubic.gemma.core.loader.util.parser |
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| ubic.gemma.core.loader.util.sdo |
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| ubic.gemma.core.logging.log4j |
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| ubic.gemma.core.metrics |
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| ubic.gemma.core.metrics.binder |
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| ubic.gemma.core.metrics.binder.cache |
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| ubic.gemma.core.metrics.binder.database |
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| ubic.gemma.core.metrics.binder.jpa |
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| ubic.gemma.core.ontology |
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| ubic.gemma.core.ontology.jena |
This package contains all the Jena-related code for ontologies that Gemma needs.
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| ubic.gemma.core.ontology.providers |
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| ubic.gemma.core.profiling |
Classes and utilities for profiling the performance of Gemma.
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| ubic.gemma.core.search |
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| ubic.gemma.core.search.lucene |
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| ubic.gemma.core.search.source |
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| ubic.gemma.core.security |
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| ubic.gemma.core.security.audit |
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| ubic.gemma.core.security.authentication |
This package contains implementation of gsec UserService and gemma.gsec.authentication.UserManager.
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| ubic.gemma.core.security.authorization.acl |
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| ubic.gemma.core.tasks |
This package contains task definitions.
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| ubic.gemma.core.tasks.analysis.coexp |
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| ubic.gemma.core.tasks.analysis.diffex |
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| ubic.gemma.core.tasks.analysis.expression |
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| ubic.gemma.core.tasks.analysis.sequence |
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| ubic.gemma.core.tasks.maintenance |
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| ubic.gemma.core.tasks.visualization |
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| ubic.gemma.core.util |
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| ubic.gemma.core.util.concurrent |
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| ubic.gemma.core.util.locking |
Utilities for locking files.
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| ubic.gemma.core.visualization |
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| ubic.gemma.model.analysis |
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| ubic.gemma.model.analysis.expression |
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| ubic.gemma.model.analysis.expression.coexpression |
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| ubic.gemma.model.analysis.expression.diff |
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| ubic.gemma.model.analysis.expression.pca |
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| ubic.gemma.model.annotations |
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| ubic.gemma.model.association |
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| ubic.gemma.model.association.coexpression |
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| ubic.gemma.model.blacklist |
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| ubic.gemma.model.common |
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| ubic.gemma.model.common.auditAndSecurity |
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| ubic.gemma.model.common.auditAndSecurity.curation |
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| ubic.gemma.model.common.auditAndSecurity.eventType |
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| ubic.gemma.model.common.description |
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| ubic.gemma.model.common.measurement |
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| ubic.gemma.model.common.protocol |
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| ubic.gemma.model.common.quantitationtype |
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| ubic.gemma.model.common.search |
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| ubic.gemma.model.expression.arrayDesign |
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| ubic.gemma.model.expression.bioAssay |
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| ubic.gemma.model.expression.bioAssayData |
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| ubic.gemma.model.expression.biomaterial |
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| ubic.gemma.model.expression.designElement |
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| ubic.gemma.model.expression.experiment |
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| ubic.gemma.model.genome |
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| ubic.gemma.model.genome.biosequence |
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| ubic.gemma.model.genome.gene |
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| ubic.gemma.model.genome.sequenceAnalysis |
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| ubic.gemma.model.util |
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| ubic.gemma.persistence |
This package contains classes related to retrieval and persistence of entities.
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| ubic.gemma.persistence.cache |
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| ubic.gemma.persistence.hibernate |
This package contains Hibernate-related classes and utilities for persisting entities.
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| ubic.gemma.persistence.initialization |
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| ubic.gemma.persistence.persister |
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| ubic.gemma.persistence.retry |
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| ubic.gemma.persistence.service |
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| ubic.gemma.persistence.service.analysis |
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| ubic.gemma.persistence.service.analysis.expression |
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| ubic.gemma.persistence.service.analysis.expression.coexpression |
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| ubic.gemma.persistence.service.analysis.expression.diff |
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| ubic.gemma.persistence.service.analysis.expression.pca |
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| ubic.gemma.persistence.service.analysis.expression.sampleCoexpression |
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| ubic.gemma.persistence.service.association |
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| ubic.gemma.persistence.service.association.coexpression |
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| ubic.gemma.persistence.service.blacklist |
Service for managing blacklisted entities.
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| ubic.gemma.persistence.service.common |
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| ubic.gemma.persistence.service.common.auditAndSecurity |
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| ubic.gemma.persistence.service.common.auditAndSecurity.curation |
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| ubic.gemma.persistence.service.common.description |
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| ubic.gemma.persistence.service.common.measurement |
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| ubic.gemma.persistence.service.common.protocol |
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| ubic.gemma.persistence.service.common.quantitationtype |
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| ubic.gemma.persistence.service.expression.arrayDesign |
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| ubic.gemma.persistence.service.expression.bioAssay |
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| ubic.gemma.persistence.service.expression.bioAssayData |
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| ubic.gemma.persistence.service.expression.biomaterial |
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| ubic.gemma.persistence.service.expression.designElement |
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| ubic.gemma.persistence.service.expression.experiment |
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| ubic.gemma.persistence.service.genome |
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| ubic.gemma.persistence.service.genome.biosequence |
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| ubic.gemma.persistence.service.genome.gene |
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| ubic.gemma.persistence.service.genome.sequenceAnalysis |
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| ubic.gemma.persistence.service.genome.taxon |
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| ubic.gemma.persistence.service.maintenance |
Contains classes related to database maintenance.
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| ubic.gemma.persistence.util |
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