Uses of Package
ubic.gemma.core.util.matrix

Packages that use ubic.gemma.core.util.matrix

Package	Description
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess	This package contains classes for preprocessing expression data.
ubic.gemma.core.analysis.preprocess.normalize
ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.analysis.service
ubic.gemma.core.datastructure.matrix	This package contains data structures for representing matrices of gene expression.
ubic.gemma.core.loader.expression	This package contains interfaces and classes for loading expression data.
ubic.gemma.core.loader.expression.simple
ubic.gemma.core.ontology
ubic.gemma.core.util
ubic.gemma.core.util.graphics
ubic.gemma.core.util.math
ubic.gemma.core.util.math.linalg
ubic.gemma.core.util.math.linearmodels
ubic.gemma.core.util.matrix	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).
ubic.gemma.core.util.matrix.datafilter
ubic.gemma.persistence.service.analysis.expression.pca
ubic.gemma.persistence.service.analysis.expression.sampleCoexpression
ubic.gemma.rest

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.core.analysis.expression.diff

Class	Description
DoubleMatrix	Abstract base class for 2D matrices of double values with named columns and rows.
ObjectMatrix

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.core.analysis.preprocess

Class	Description
DoubleMatrix	Abstract base class for 2D matrices of double values with named columns and rows.

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.core.analysis.preprocess.normalize

Class	Description
DoubleMatrix	Abstract base class for 2D matrices of double values with named columns and rows.

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.core.analysis.preprocess.svd

Class	Description
DoubleMatrix	Abstract base class for 2D matrices of double values with named columns and rows.

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.core.analysis.service

Class	Description
DoubleMatrix	Abstract base class for 2D matrices of double values with named columns and rows.

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.core.datastructure.matrix

Class	Description
DoubleMatrix	Abstract base class for 2D matrices of double values with named columns and rows.

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.core.loader.expression

Class	Description
DoubleMatrix	Abstract base class for 2D matrices of double values with named columns and rows.

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.core.loader.expression.simple

Class	Description
DoubleMatrix	Abstract base class for 2D matrices of double values with named columns and rows.

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.core.ontology

Class	Description
DoubleMatrix	Abstract base class for 2D matrices of double values with named columns and rows.

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.core.util

Class	Description
DoubleMatrix	Abstract base class for 2D matrices of double values with named columns and rows.

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.core.util.graphics

Class	Description
DoubleMatrix	Abstract base class for 2D matrices of double values with named columns and rows.

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.core.util.math

Class	Description
DoubleMatrix	Abstract base class for 2D matrices of double values with named columns and rows.
SparseDoubleMatrix	A sparse matrix that knows about row and column names.

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.core.util.math.linalg

Class	Description
DoubleMatrix	Abstract base class for 2D matrices of double values with named columns and rows.

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.core.util.math.linearmodels

Class	Description
DoubleMatrix	Abstract base class for 2D matrices of double values with named columns and rows.
ObjectMatrix
StringMatrix	A NamedMatrix containing String objects.

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.core.util.matrix

Class	Description
AbstractMatrix
AbstractMatrixReader	Abstract class representing an object that can read in a Matrix2D from a file.
CompressedSparseDoubleMatrix	Supports sparse matrices (where sparse means most values are zero, not that they are missing).
DenseDoubleMatrix	A dense matrix of doubles that knows about row and column names.
DoubleMatrix	Abstract base class for 2D matrices of double values with named columns and rows.
FastRowAccessDoubleMatrix	Dense 2D matrix implementation designed for very fast access of entire rows.
Matrix2D	Represents a matrix with index columns and rows.
ObjectMatrix
ObjectMatrixImpl	Matrix that can hold any type of object
PrimitiveMatrix	Matrix that holds primitives, with an available object representation of the values.
SparseDoubleMatrix	A sparse matrix that knows about row and column names.
StringMatrix	A NamedMatrix containing String objects.

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.core.util.matrix.datafilter

Class	Description
Matrix2D	Represents a matrix with index columns and rows.

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.persistence.service.analysis.expression.pca

Class	Description
DoubleMatrix	Abstract base class for 2D matrices of double values with named columns and rows.

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.persistence.service.analysis.expression.sampleCoexpression

Class	Description
DoubleMatrix	Abstract base class for 2D matrices of double values with named columns and rows.

Classes in ubic.gemma.core.util.matrix used by ubic.gemma.rest

Class	Description
DoubleMatrix	Abstract base class for 2D matrices of double values with named columns and rows.