# Estimate Systems Immune Response from RNA-seq data

## Documentation for package ‘easier’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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