Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments

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Documentation for package ‘lute’ version 1.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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bisqueParam	Make new object of class bisqueParam
BisqueParam-class	bisqueParam-class
bisqueParam-class	bisqueParam-class
cellProportionsPredictions	Make new cellProportionsPredictions object.
cellProportionsPredictions-class	cellProportionsPredictions-class
deconParam-class	deconvolutionParam-class
DeconParam-class,	deconvolutionParam-class
Deconvolute	deconvolution
deconvolute,	deconvolution
deconvolution	deconvolution
Deconvolution,	deconvolution
deconvolution-method	Deconvolution method for bisqueParam
deconvolution-method	Deconvolution generic behavior for object of class deconvolutionParam
deconvolution-method	Deconvolution method for class independentbulkParam
deconvolution-method	Deconvolution method for nnlsParam
deconvolution-method	Deconvolution generic behavior for object of class referencebasedParam
deconvolutionParam-class	deconvolutionParam-class
DeconvolutionParam-class,	deconvolutionParam-class
eset_to_sce	eset_to_sce Convert ExpressionSet to SingleCellExperiment.
eset_to_se	eset_to_se
findmarkersParam	Make new object of class findmarkersParam
findMarkersParam-class	findmarkersParam-class
findmarkersParam-class	findmarkersParam-class
FindmarkersParam-class,	findmarkersParam-class
getDeconvolutionExampleData	getDeconvolutionExampleData
getDeconvolutionExampleDataBisque	getDeconvolutionExampleDataBisque
getDeconvolutionExampleDataSCDC	getDeconvolutionExampleDataSCDC
get_celltypes_from_sce	get_celltypes_from_sce
get_csf_reference	get_csf_reference
get_eset_from_matrix	get_eset_from_matrix
independentbulkParam	Make a new independentbulkParam object
independentbulkParam-class	independentbulkParam-class
lute	lute framework
luteSupportedDeconvolutionAlgorithms	luteSupportedDeconvolutionAlgorithms
new_workflow_table	new_workflow_table
nnlsParam	Make new object of class nnlsParam
NNLSParam-class	nnlsParam-class
nnlsParam-class	nnlsParam-class
parseDeconvolutionPredictionsResults	parseDeconvolutionPredictionsResults
proportionsVectorsList	proportionsVectorsList
randomMarkersVectorsList	randomMarkersVectorsList
randomSingleCellExperiment	randomSingleCellExperiment
referencebasedParam	Make new object of class referencebasedParam
referencebasedParam-class	referencebasedParam-class
referenceFromSingleCellExperiment	referenceFromSingleCellExperiment
rmse	rmse
rmseTest	rmseTest
sce_to_eset	sce_to_eset Convert SingleCellExperiment to ExpressionSet.
sce_to_se	sce_to_se Convert SingleCellExperiment to SummarizedExperiment.
se_to_eset	se_to_eset
se_to_sce	se_to_sce
show-method	Show generic behavior for object of class bisqueParam
show-method	Inspect cellProportionsPredictions object.
show-method	Show generic behavior for object of class deconvolutionParam
show-method	Show generic behavior for object of class findmarkersParam
show-method	Method for independentbulkParam
show-method	Show generic behavior for object of class nnlsParam
show-method	Show generic behavior for object of class referencebasedParam
show-method	Show generic behavior for object of class typemarkersParam
TypeMarkers	typemarkers
typemarkers	typemarkers
Typemarkers,	typemarkers
typemarkers-method	Cell type markers method for findmarkersParam
typemarkers-method	Method for class typemarkersParam
typemarkersParam	Make new object of class typemarkersParam
TypeMarkersParam-class	typemarkersParam-class
typemarkersParam-class	typemarkersParam-class
TypemarkersParam-class,	typemarkersParam-class
ypb_from_sce	ypb_from_sce
z_matrix_from_sce	z_matrix_from_sce
[[-method	Inspect slot in deconvolutionParam object
[[-method	Inspect slot in typemarkersParam object