All Packages
Package Summary
Package
Description
This package contains built-in Gemma CLI applications.
Utilities for executing batch jobs via the CLI.
This package provides completion support for the Gemma CLI.
This package contains reusable command line options.
This package contains classes for preprocessing expression data.
Convert data from one
QuantitationType to another.This package contains classes for detecting and linting expression data.
This package contains classes for filtering expression data.
This package provides capabilities for slicing
BulkExpressionDataVector.This package contains classes for analysing single-cell expression data.
This package contains classes for subsetting and aggregating single-cell data.
This package contains classes for computing various statistics.
This package contains classes that are used to manage Gemma's Spring context.
This package contains classes that are used to manage Gemma's Spring context.
This package contains data structures for representing matrices of gene expression.
This package contains I/O utilities for reading and writing expression data matrices.
This package contains sparse data structures implementations and utilities.
Provides functionalities for running background tasks.
This package contains interfaces and classes for loading expression data.
This package contains classes for loading expression data from CELLxGENE.
Provides classes for fetching data from various sources.
This package contains specific logic for dealing with single-cell data from GEO.
This package contains interfaces and classes for loading sequencing data.
Model classes for loading simple expression data.
This package contains classes for loading single-cell expression data.
This package contains classes for loading single-cell metadata such as cell type assignment and cell-level
characteristics.
This package contains classes for transforming single-cell expression data.
This package contains interfaces and classes for loading expression data from Synapse.
This package contains utilities for loading and interacting with the UCSC Cell Browser.
This package contains interfaces and classes for loading expression data from Zenodo.
Provides classes for fetching data from various sources.
Utilities for working with FTP.
Minimalistic read-only wrapper around HDF5 native library.
Utilities for mapping
Identifiable entities to external identifiers.Jena-based ontology implementation:
OntologyService
concrete classes, Lucene indexer, OWL/OBO/RO/IAO helpers.This package contains baseCode built-in ontologies and a
ubic.basecode.ontology.providers.GenericOntologyService
to implement your own ontologies.In-Gemma ontology full-text search subsystem.
Simple ontology implementation.
Classes and utilities for profiling the performance of Gemma.
Mass-indexer driver around Hibernate Search 7's
MassIndexer.Gsec is an attempt to generalise the security framework of Gemma to make it usable in other projects such as
ASPIREdb.
Provides various implementations of AbstractAclProvider for filtering method return values for ACLS.
This package contains task definitions.
Utilities for locking files.
Labelled-axis matrix types ported in-tree from baseCode's
ubic.basecode.dataStructure.matrix subsystem as part of the Phase 3
baseCode retirement (see BASECODE_MATRIX_RECCE.md and
BASECODE_DEP_AUDIT.md).Utilities for accessing extended runtime information.
This package contains classes related to the Cell Browser visualization tool.
This package contains Hibernate-related classes and utilities for persisting entities.
Service for managing blacklisted entities.
Contains classes related to database maintenance.