Gemma 1.32.3 API
Packages
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 can be used by other Java packages to include CLIs.
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 provides capabilities for slicing
BulkExpressionDataVector.This package contains classes for analysing single-cell expression data.
This package contains classes for splitting 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.
Provides functionalities for running background tasks.
This package contains interfaces and classes for loading expression data.
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.
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.This package contains all the Jena-related code for ontologies that Gemma needs.
Classes and utilities for profiling the performance of Gemma.
This package contains task definitions.
Utilities for locking files.
This package contains classes related to the Cell Browser visualization tool.
This package contains model classes for Gemma.
This package contains classes related to retrieval and persistence of entities.
This package contains Hibernate-related classes and utilities for persisting entities.
Service for managing blacklisted entities.
Contains classes related to database maintenance.
This package contains classes related to static assets management, such as CSS and JavaScript files.