Man pages for korkutlab/imogimap
What the Package Does (One Line, Title Case)
| AG_gene_list | Angiogenesis signature genes |
| calculate_syng_score | Calculates a synergy score given median and standard error of... |
| EMT_gene_list | EMT signature genes |
| find_a_synergy | Evalues synergies for a data frame containing values of an... |
| get_angio_score | Calculates Angiogenesis score |
| get_emt_score | Calculates Epithelial Mesenchymal transition (EMT) score |
| get_features | Calculates and transforms default immune features within a... |
| get_ifng_score | Calculates a score for IFNG expression |
| get_quantile_rank | Stratify each column of data using quantile values. |
| get_selected_features | Calculates and transforms default immune features within a... |
| get_sensitivity | Calculation and statistical assessment of synergistic... |
| get_specificity | Calculation and statistical assessment of synergistic... |
| get_TCI_score | Calculates a T cell inflammation score |
| icp_gene_list | Default list of immune checkpoints |
| im_boxplot | Generate a stratified boxplot for immune feature values |
| im_boxplot_tcga | Generates a stratified boxplot for immune feature values... |
| im_boxplot_tcga_plot | Plot data from im_bloxplot_tcga |
| im_cor | Calculate Spearman correlation with immune checkpoints |
| im_cor_tcga | Finds Spearman correlation between an oncogene, an immune... |
| im_netplot | Creates and plot an igraph network from dataframe |
| imogimap | imogimap: Immuno-oncology gene expression assessment. |
| im_syng | Find combinatorial association of immunotherapy co-targets... |
| im_syng_tcga | Calculation and statistical assessment of synergistic... |
| im_syng_tcga_shiny | Equivalent of im_syng_TCGA ro run with shiny app |
| round_df | Round the numeric columns in a data.frame |
| sample_immune_cell_fraction_data | Sample data set for immune cell fraction data |
| sample_Leukocyte_fraction_data | Sample Leukocyte fraction data |
| sample_mRNA_data | Sample mRNA expression data |
| TCGA_disease_list | TCGA disease names |
| TCGA_IMCell_fraction | Immune cell type fractions for TCGA data |
| TCGA_immune_features_list | TCGA immune features list |
| TCGA_Leukocyte_fraction | TCGA Leukocyte fractions |
| TCGA_TMB | Tumor mutation burden |
