Calculate EMT Scores Based on Omics Data

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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