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

## Documentation for package ‘scAnnotatR’ version 1.0.0

- 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
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