# Calculate EMT Scores Based on Omics Data

## Documentation for package ‘EMTscore’ version 0.99.10

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

## Help Pages

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