add_EMT_score           Add EMT Scores to Seurat or SCE Objects
add_EMT_score_Bulk      Compute EMT scores for one or multiple bulk
                        expression matrices
add_EMT_score_multiple
                        Add Multiple EMT Scores to Seurat or SCE
                        Objects
Arrange_plots           Arrange multiple ggplot objects with subtitles
                        and common legend
cell_annotation_file    Cell-line annotation table
compute_Signature_score
                        Compute Signature Score from Bulk Matrix or
                        Seurat Object
compute_Signature_score_SingleCell
                        Compute Multiple Signature Scores for
                        Single-Cell Objects
correlate_sample_scores
                        Calculate correlations between pathway or
                        signature scores across samples
data_for_plot           Example data prepared for plotting
data_prepare            Prepare data for plotting
Execute_AUCell          Execute AUCell Scoring from GMT File
Execute_AUCell_parallel
                        Compute AUCell Scores for Multiple Gene Sets
Execute_E_M_plot        Plot E vs M scores
Execute_GSVA            Execute GSVA Scoring from GMT File
Execute_GSVA_parallel   Compute GSVA Scores for Multiple Gene Sets in
                        Parallel
Execute_JAS             Execute JASMINE Scoring from GMT File
Execute_JASMINE_parallel
                        Compute JASMINE Scores for Multiple Gene Sets
                        in Parallel
Execute_M_dimension_plot
                        Plot M dimension scores
Execute_nnPCA           Execute Non-Negative Sparse PCA (nnPCA) Scoring
Execute_nnPCA_parallel
                        Compute nnPCA Scores for Multiple Gene Sets in
                        Parallel
Execute_SCSE            Execute SCSE Scoring from GMT File
Execute_SCSE_parallel   Compute SCSE Scores for Multiple Gene Sets
Execute_ssGSEA          Execute ssGSEA Scoring from GMT File
Execute_ssGSEA_parallel
                        Compute ssGSEA Scores for Multiple Gene Sets in
                        Parallel
filter_gmt_by_reference
                        Filter a GMT file by overlap with a reference
                        GMT
geneExp                 Example gene expression matrix
GO                      Gene Ontology EMT-related gene sets
MSigDB_Hallmark         MSigDB Hallmark gene sets
nnPCA_Result_EMT        nnPCA_Result_EMT
nnPCA_Result_multiple   Example multiple nnPCA results
Panchy_et_al_E_signature
                        Panchy et al. epithelial signature
Panchy_et_al_M_signature
                        Panchy et al. mesenchymal signature
plot_EMT_from_objects   Plot EMT Scores Along Pseudotime from Seurat
                        Objects
plot_heatmap_function   present result of heat map of genes that
                        contribute to M score of dimension 1 and
                        disension 2
predict_cluster_labels
                        Predict Cluster Labels from PCA Results Using
                        GMM or Kmeans
read_gmt                Read GMT File and Extract Genes
SCSE_Result_EMT         Example SCSE EMT scores
Tan_et_al_cell_line_E_signature
                        Tan et al. cell-line epithelial signature
Tan_et_al_cell_line_M_signature
                        Tan et al. cell-line mesenchymal signature
Tan_et_al_tumor_E_signature
                        Tan et al. tumor epithelial signature
Tan_et_al_tumor_M_signature
                        Tan et al. tumor mesenchymal signature
write_gmt               Write Gene Sets to a GMT File
