# Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments

## Documentation for package ‘lute’ version 1.2.0

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

## Help Pages

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