assess_immune_response
                        Assess easier score as predictor of patients'
                        immune response
calc_z_score            Perform matrix Z-score normalization
categorize_TMB          Define tumor mutational burden (TMB)
                        categories.
compute_Ayers_expIS     Compute Expanded Immune signature (Ayers_expIS)
                        score
compute_CC_pairs        Compute cell-cell interactions scores using
                        computed ligand-receptor weights
compute_CCpair_score    Compute cell-cell pair score
compute_CYT             Compute cytolytic activity (CYT) score
compute_Davoli_IS       Compute Davoli immune signature (Davoli_IS)
                        score
compute_IFNy            Compute IFNy signature (IFNy) score
compute_IMPRES_MSI      Compute Immuno-Predictive Score (IMPRES) and
                        Micro Satellite Instability (MSI) status score
compute_LR_pairs        Compute ligand-receptor pair weights from TPM
                        bulk gene expression
compute_RIR             Compute three scores from the immune resistance
                        program: resF_down (RIR), resF_up, resF
                        (resF_up - resF_down)
compute_Roh_IS          Compute Roh immune score (Roh_IS)
compute_TF_activity     Compute transcription factor activity from gene
                        expression using DoRothEA
compute_TLS             Computation of tertiary lymphoid structures
                        signature (TLS) score
compute_Tcell_inflamed
                        Compute T cell-inflamed signature
                        (Tcell_inflamed) score
compute_cell_fractions
                        Compute immune cell fractions from gene
                        expression using quanTIseq
compute_chemokines      Compute chemokine signature (chemokines) score
compute_pathway_activity
                        Compute pathway activity from gene expression
                        using PROGENy
compute_scores_immune_response
                        Compute published scores of immune response
discretize              Converts a continuous variable into categorical
easier-pkg              easier: predicting immune response by using
                        quantitative descriptors of the tumor
                        microenvironment extracted from RNA-seq data.
explore_biomarkers      Explore biomarkers of immune response
get_OE_bulk             Compute overall expression (OE) of the immune
                        resistance program used in the computation of
                        repressed immune resistance signature (RIR)
                        score.
get_semi_random_OE      Compute random scores of the immune resistance
                        program used in the computation of repressed
                        immune resistance signature (RIR) score.
predict_immune_response
                        Compute predicted immune response
predict_with_rmtlr      Predict single-view immune response
reannotate_genes        Gene re-annotation using HGNC symbols
retrieve_easier_score   Retrieve easier scores of immune response
rmtlr_test              Regularized Multi-Task Linear Regression
                        (RMTLR) model predictions
