Man pages for olapuentesantana/easier_manuscript
Evaluate patient immune response to ICBs through a systems approach
| bemkl_supervised_multioutput_regression_variational_test | BEMKL algorithm uses the training model parameters on the... |
| compare_immune_response | Comparison of the actual predictions based on different... |
| compute.Ayers_expIS | Compute Expanded Immune signature |
| compute_CCpair_score | compute_CCpair_score |
| compute_CC_pairs_grouped | compute_CC_pairs_grouped |
| compute_cell_fractions | Compute immune cell fractions |
| compute.chemokines | Compute chemokine score |
| compute.CYT | Compute cytolytic activity score |
| compute.Davoli_IS | Compute Davoli immune signature |
| compute_gold_standards | Compute gold standards |
| compute_ICB_genes | Compute the expression of the immune checkpoints genes |
| compute.IFNy | Compute IFNy signature score |
| compute.IMPRES | Compute Immuno-Predictive Score (IMPRES) |
| compute_LR_pairs | Compute ligand-receptor pairs |
| compute.MSI | Compute MSI score |
| compute_pathways_scores | Compute pathways score |
| compute.RIR | Compute Immune resistance program |
| compute.Roh_IS | Compute Roh immune score |
| compute.Tcell_inflamed | Compute T cell-inflamed signature score |
| compute_TF_activity | Compute transription factors activity |
| compute.TLS | Compute tertiary lymphoid structures signature |
| explore_biomarkers | Examination of possible relevant biomarkers in cancer dataset |
| get_OE_bulk | Calculate overall expression (OE) |
| get_semi_random_OE | Calculate random scores |
| ipsmap | Calculate Immunophenoscore value |
| multi_task_EN_test | Multi-task elastic net algorithm implements the model... |
| predict_immune_response | Immune response prediction |
| predict_with_bemkl | Make predictions using BEMKL |
| predict_with_multitaskelasticnet | Make predictions using multi-task elastic net |
| standarization | Calculation of a matrix z-score from scratch. |
