API for IOBR
Immune Oncology Biological Research
| Global functions | |
|---|---|
| .add_tme_scores | Source code |
| .appendSignatures | Man page Source code |
| .build_cor_plot | Source code |
| .build_heatmap_colors | Source code |
| .build_mut_matrices | Man page Source code |
| .calculate_tpm | Source code |
| .classify_degs | Source code |
| .convert_to_colors | Source code |
| .create_mut_matrix | Man page Source code |
| .filter_signatures | Source code |
| .format_deconv_result | Source code |
| .get_ensembl_features | Source code |
| .get_entrez_features | Source code |
| .get_gene_sets | Source code |
| .get_group_colors | Source code |
| .get_hugo_features | Source code |
| .get_lengths_from_biomart | Source code |
| .get_lengths_from_df | Source code |
| .get_lengths_human | Source code |
| .get_lengths_local | Source code |
| .get_lengths_mouse | Source code |
| .get_probeset_features | Source code |
| .match_and_extract_lengths | Source code |
| .onAttach | Source code |
| .onLoad | Source code |
| .palette_box | Source code |
| .palette_continue | Source code |
| .palette_continue2 | Source code |
| .palette_heatmap | Source code |
| .palette_heatmap3 | Source code |
| .palette_random | Source code |
| .palette_tidyheatmap | Source code |
| .pie_chart_basic | Source code |
| .pie_chart_donut | Source code |
| .pie_chart_piedonut | Source code |
| .prepare_cor_data | Source code |
| .prepare_pdata | Source code |
| .process_gsea_results | Source code |
| .roc_single_var | Source code |
| .roc_three_vars | Source code |
| .roc_two_vars | Source code |
| .run_deseq2 | Source code |
| .run_limma | Source code |
| .save_cor_plot | Source code |
| .surv_plot_binary | Source code |
| .surv_plot_multi | Source code |
| BinomialAUC | Man page Source code |
| BinomialModel | Man page Source code |
| CIBERSORT | Man page Source code |
| CalculatePref | Man page Source code |
| CalculateTimeROC | Man page Source code |
| Construct_con | Man page Source code |
| ConvertRownameToLoci | Man page Source code |
| CoreAlg | Man page Source code |
| DClsei | Man page Source code |
| DCrr | Man page Source code |
| DrawQQPlot | Man page Source code |
| EPIC | Man page Source code |
| Enet | Man page Source code |
| GetFractions.Abbas | Man page Source code |
| GetOutlierGenes | Man page Source code |
| IPS_calculation | Man page Source code |
| LR_cal | Man page Source code |
| MCPcounter.estimate | Man page Source code |
| ParseInputExpression | Man page Source code |
| PlotAUC | Man page Source code |
| PlotTimeROC | Man page Source code |
| ProcessingData | Man page Source code |
| PrognosticAUC | Man page Source code |
| PrognosticModel | Man page Source code |
| PrognosticResult | Man page Source code |
| RegressionResult | Man page Source code |
| RemoveBatchEffect | Man page Source code |
| SplitTrainTest | Man page Source code |
| Top_probe | Man page Source code |
| add_iobr_mirror | Man page Source code |
| add_riskscore | Man page Source code |
| anno_eset | Man page Source code |
| assimilate_data | Man page Source code |
| batch_cor | Man page Source code |
| batch_kruskal | Man page Source code |
| batch_pcc | Man page Source code |
| batch_sig_surv_plot | Man page Source code |
| batch_surv | Man page Source code |
| batch_wilcoxon | Man page Source code |
| best_cutoff | Man page Source code |
| best_cutoff2 | Man page Source code |
| calculate_break_month | Man page Source code Source code |
| calculate_sig_score | Man page Source code |
| calculate_sig_score_integration | Man page Source code |
| calculate_sig_score_pca | Man page Source code |
| calculate_sig_score_ssgsea | Man page Source code |
| calculate_sig_score_zscore | Man page Source code |
| cell_bar_plot | Man page Source code |
| check_cancer_types | Man page Source code |
| check_eset | Man page Source code |
| clear_iobr_cache | Man page Source code |
| combine_pd_eset | Man page Source code |
| count2tpm | Man page Source code |
| creat_folder | Man page Source code |
| deconvo_cibersort | Man page Source code |
| deconvo_epic | Man page Source code |
| deconvo_estimate | Man page Source code |
| deconvo_ips | Man page Source code |
| deconvo_mcpcounter | Man page Source code |
| deconvo_quantiseq | Man page Source code |
| deconvo_ref | Man page Source code |
| deconvo_timer | Man page Source code |
| deconvo_tme | Man page Source code |
| deconvo_xcell | Man page Source code |
| deconvolute_quantiseq.default | Man page Source code |
| deconvolute_timer.default | Man page Source code |
| design_mytheme | Man page Source code |
| doPerm | Man page Source code |
| download_iobr_data | Man page Source code |
| enrichment_barplot | Man page Source code |
| eset_distribution | Man page Source code |
| estimateScore | Man page Source code |
| exact_pvalue | Man page Source code |
| extract_sc_data | Man page Source code |
| feature_manipulation | Man page Source code |
| feature_select | Man page Source code |
| filterCommonGenes | Man page Source code |
| find_markers_in_bulk | Man page Source code |
| find_mutations | Man page Source code |
| find_outlier_samples | Man page Source code |
| find_variable_genes | Man page Source code |
| fixMixture | Man page Source code |
| format_msigdb | Man page Source code |
| format_signatures | Man page Source code |
| generateRef | Man page Source code |
| generateRef_DEseq2 | Man page Source code |
| generateRef_limma | Man page Source code |
| generateRef_rnaseq | Man page Source code |
| generateRef_seurat | Man page Source code |
| getHRandCIfromCoxph | Man page Source code |
| get_cols | Man page Source code |
| get_cor | Man page Source code |
| get_cor_matrix | Man page Source code |
| get_default_mirrors | Man page Source code |
| get_iobr_cache_dir | Man page Source code |
| get_sig_sc | Man page Source code |
| gsva_use_new_api | Man page Source code |
| high_var_fea | Man page Source code |
| imvigor210_pdata | Man page |
| iobr_cor_plot | Man page Source code |
| iobr_deconvo_pipeline | Man page Source code |
| iobr_deg | Man page Source code |
| iobr_pca | Man page Source code |
| ipsmap | Man page Source code |
| lasso_select | Man page Source code |
| limma.dif | Man page Source code |
| list_github_datasets | Man page Source code |
| list_iobr_mirrors | Man page Source code |
| load_data | Man page Source code |
| log2eset | Man page Source code |
| makeQN | Man page Source code |
| make_mut_matrix | Man page Source code |
| mapGenes | Man page Source code |
| mapbw | Man page Source code |
| mapcolors | Man page Source code |
| merge_duplicate | Man page Source code |
| merge_duplicates | Man page Source code |
| merge_eset | Man page Source code |
| microenvironmentScores | Man page Source code |
| mouse2human_eset | Man page Source code |
| null_models | Man page |
| outputGCT | Man page Source code |
| output_sig | Man page Source code |
| palettes | Man page Source code |
| parallel_doperm | Man page Source code |
| patterns_to_na | Man page |
| pdata_stad | Man page |
| percent_bar_plot | Man page Source code |
| pie_chart | Man page Source code |
| plotPurity | Man page Source code |
| quanTIseq | Man page Source code |
| quantiseq_helper | Man page |
| random_strata_cells | Man page Source code |
| rawEnrichmentAnalysis | Man page Source code |
| rbind_iobr | Man page Source code |
| remove_batcheffect | Man page Source code |
| remove_duplicate_genes | Man page Source code |
| remove_names | Man page Source code |
| reset_iobr_cache_dir | Man page Source code |
| reset_iobr_mirrors | Man page Source code |
| roc_time | Man page Source code |
| scaleCounts | Man page Source code |
| scale_matrix | Man page Source code |
| select_method | Man page Source code |
| set_iobr_cache_dir | Man page Source code |
| sigScore | Man page Source code |
| sig_box | Man page Source code |
| sig_box_batch | Man page Source code |
| sig_forest | Man page Source code |
| sig_group | Man page |
| sig_gsea | Man page Source code |
| sig_heatmap | Man page Source code |
| sig_pheatmap | Man page Source code |
| sig_roc | Man page Source code |
| sig_surv_plot | Man page Source code |
| signature_collection | Man page |
| signature_score_calculation_methods | Man page |
| spillOver | Man page Source code |
| stad_group | Man page |
| subgroup_data | Man page |
| subgroup_survival | Man page Source code |
| surv_group | Man page Source code |
| tcga_rna_preps | Man page Source code |
| tcga_stad_pdata | Man page |
| test_for_infiltration | Man page Source code |
| timer_available_cancers | Man page |
| timer_info | Man page Source code |
| tme_cluster | Man page Source code |
| tme_deconvolution_methods | Man page |
| transformScores | Man page Source code |
| transform_data | Man page Source code |
| xCellAnalysis | Man page Source code |
| xCellSignifcanceBetaDist | Man page Source code |
| xCellSignifcanceRandomMatrix | Man page Source code |
