Estimate Systems Immune Response from RNA-seq data

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Documentation for package ‘easier’ version 1.15.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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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_CCpair_score	Compute cell-cell pair score
compute_CC_pairs	Compute cell-cell interactions scores using computed ligand-receptor weights
compute_cell_fractions	Compute immune cell fractions from gene expression using quanTIseq
compute_chemokines	Compute chemokine signature (chemokines) 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_pathway_activity	Compute pathway activity from gene expression using PROGENy
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_scores_immune_response	Compute published scores of immune response
compute_Tcell_inflamed	Compute T cell-inflamed signature (Tcell_inflamed) score
compute_TF_activity	Compute transcription factor activity from gene expression using DoRothEA
compute_TLS	Computation of tertiary lymphoid structures signature (TLS) score
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