Pretrained learning models for cell type prediction on single cell RNA-sequencing data

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Documentation for package ‘scAnnotatR’ version 1.11.0

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

Help Pages

balance_dataset	Internal functions of scAnnotatR package
caret_model	caret_model
caret_model<-	Internal functions of scAnnotatR package
caret_model<--method	Internal functions of scAnnotatR package
cell_type	cell_type
cell_type<-	Setter for cell_type. Change cell type of a classifier
cell_type<--method	cell_type
checkCaretModelValidity	Internal functions of scAnnotatR package
checkCellTypeValidity	Internal functions of scAnnotatR package
checkMarkerGenesValidity	Internal functions of scAnnotatR package
checkObjectValidity	Internal functions of scAnnotatR package
checkParentValidity	Internal functions of scAnnotatR package
checkPThresValidity	Internal functions of scAnnotatR package
check_parent_child_coherence	Internal functions of scAnnotatR package
classify_cells	Classify cells from multiple models
classify_cells_sce	Internal functions of scAnnotatR package
classify_cells_seurat	Internal functions of scAnnotatR package
classify_clust	Internal functions of scAnnotatR package
construct_tag_vect	Internal functions of scAnnotatR package
delete_model	Delete model/branch from package
download_data_file	Internal functions of scAnnotatR package
filter_cells	Internal functions of scAnnotatR package
load_models	Load classifiers from databases
make_prediction	Internal functions of scAnnotatR package
marker_genes	marker_genes
marker_genes<-	Internal functions of scAnnotatR package
marker_genes<--method	Internal functions of scAnnotatR package
parent	parent
parent<-	Internal functions of scAnnotatR package
parent<--method	Internal functions of scAnnotatR package
plant_tree	Plant tree from list of models
plot_roc_curve	Plot roc curve
preprocess_sce_object	Internal functions of scAnnotatR package
preprocess_seurat_object	Internal functions of scAnnotatR package
process_parent_classifier	Internal functions of scAnnotatR package
p_thres	p_thres
p_thres<-	Setter for predicting probability threshold
p_thres<--method	p_thres
save_new_model	Save a model to the package
scAnnotatR	scAnnotatR class.
select_marker_genes	Internal functions of scAnnotatR package
show-method	Show object
simplify_prediction	Internal functions of scAnnotatR package
subset_models	Internal functions of scAnnotatR package
test_classifier	Testing process.
test_classifier-method	Testing process.
test_classifier_from_mat	Internal functions of scAnnotatR package
test_classifier_sce	Internal functions of scAnnotatR package
test_classifier_seurat	Internal functions of scAnnotatR package
test_performance	Internal functions of scAnnotatR package
tirosh_mel80_example	A Seurat Object Sample
train_classifier	Train cell type classifier
train_classifier_from_mat	Internal functions of scAnnotatR package
train_classifier_sce	Internal functions of scAnnotatR package
train_classifier_seurat	Internal functions of scAnnotatR package
train_func	Internal functions of scAnnotatR package
transform_to_zscore	Internal functions of scAnnotatR package
verify_parent	Internal functions of scAnnotatR package