Man pages for olapuentesantana/easier
Estimate Systems Immune Response from RNA-seq data
| 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... |
| compute_CCpair_score | Compute cell-cell pair score |
| compute_cell_fractions | Compute immune cell fractions from gene expression using... |
| 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... |
| compute_LR_pairs | Compute ligand-receptor pair weights from TPM bulk gene... |
| compute_pathway_activity | Compute pathway activity from gene expression using PROGENy |
| compute_RIR | Compute three scores from the immune resistance program:... |
| 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... |
| compute_TLS | Computation of tertiary lymphoid structures signature (TLS)... |
| discretize | Converts a continuous variable into categorical |
| easier-package | easier: Estimate Systems Immune Response from RNA-seq data |
| explore_biomarkers | Explore biomarkers of immune response |
| get_OE_bulk | Compute overall expression (OE) of the immune resistance... |
| get_semi_random_OE | Compute random scores of the immune resistance program used... |
| 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... |
