scClassify: single-cell Hierarchical Classification

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Documentation for package ‘scClassify’ version 1.14.0

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

Help Pages

.scClassifyTrainModel	The scClassifyTrainModel class
cellTypeTrain	Accessors of cellTypeTrain for scClassifyTrainModel
cellTypeTrain-method	Accessors of cellTypeTrain for scClassifyTrainModel
cellTypeTree	Accessors of cellTypeTree for scClassifyTrainModel
cellTypeTree-method	Accessors of cellTypeTree for scClassifyTrainModel
features	Accessors of features for scClassifyTrainModel
features-method	Accessors of features for scClassifyTrainModel
getN	Function to get the required N given by the accuracy and the learning curve model
learningCurve	Fit learning curve for accuracy matrix
model	Accessors of model for scClassifyTrainModel
model-method	Accessors of model for scClassifyTrainModel
modelweights	Accessors of modelweights for scClassifyTrainModel
modelweights-method	Accessors of modelweights for scClassifyTrainModel
name	Accessors of name for scClassifyTrainModel
name-method	Accessors of name for scClassifyTrainModel
plotCellTypeTree	To plot cell type tree
predict_scClassify	Testing scClassify model
predict_scClassifyJoint	Testing scClassify model (joint training)
runHOPACH	Create HOPACH tree
runSampleCal	Run sample size calculation for pilot data for reference dataset
scClassify	Train and test scClassify model
scClassifyTrainModel-class	An S4 class to stored training model for scClassify
scClassifyTrainModelList	The scClassifyTrainModelList class
scClassifyTrainModelList-class	An S4 class to stored a list of training models from scClassify
scClassify_example	Example data used in scClassify package
trainClassExample_wang	Subset of pretrained model of Wang et al.
trainClassExample_xin	Subset of pretrained model of Xin et al.
train_scClassify	Training scClassify model