Man pages for IOBR
Immune Oncology Biological Research
| add_iobr_mirror | Add Custom Download Mirror |
| add_riskscore | Add Risk Score to Dataset |
| anno_eset | Annotate Gene Expression Matrix and Remove Duplicated Genes |
| assimilate_data | Harmonize Two Data Frames by Column Structure |
| batch_cor | Batch Correlation Analysis |
| batch_kruskal | Batch Kruskal-Wallis Test |
| batch_pcc | Batch Calculation of Partial Correlation Coefficients |
| batch_sig_surv_plot | Batch Signature Survival Plot |
| batch_surv | Batch Survival Analysis |
| batch_wilcoxon | Batch Wilcoxon Rank-Sum Test Between Two Groups |
| best_cutoff | Extract Best Cutoff and Add Binary Variable to Data Frame |
| best_cutoff2 | Extract Best Cutoff and Add Binary Variable to Data Frame |
| BinomialAUC | Calculate AUC for Binomial Model |
| BinomialModel | Binomial Model Construction |
| calculate_break_month | Break Time Into Blocks |
| CalculatePref | Calculate Performance Metrics |
| calculate_sig_score | Calculate Signature Score |
| calculate_sig_score_integration | Calculate Signature Score Using Integration Method |
| calculate_sig_score_pca | Calculate Signature Score Using PCA Method |
| calculate_sig_score_ssgsea | Calculate Signature Score Using ssGSEA Method |
| calculate_sig_score_zscore | Calculate Signature Score Using Z-Score Method |
| CalculateTimeROC | Calculate Time-Dependent ROC Curve |
| cell_bar_plot | Visualize Cell Fractions as Stacked Bar Chart |
| check_cancer_types | Process Batch Table and Validate Cancer Types |
| check_eset | Check Integrity and Outliers of Expression Set |
| CIBERSORT | CIBERSORT Deconvolution Algorithm |
| clear_iobr_cache | Clear IOBR Data Cache |
| combine_pd_eset | Combine Phenotype Data and Expression Set |
| Construct_con | Construct Contrast Matrix |
| ConvertRownameToLoci | Convert Rowname To Loci |
| CoreAlg | Core Algorithm for CIBERSORT Deconvolution |
| count2tpm | Convert Read Counts to Transcripts Per Million (TPM) |
| creat_folder | Create Nested Output Folders |
| DClsei | Constrained Least Squares Deconvolution |
| DCrr | Robust Regression Deconvolution |
| deconvo_cibersort | Deconvolve Using CIBERSORT |
| deconvo_epic | Deconvolve Immune Microenvironment Using EPIC |
| deconvo_estimate | Calculate ESTIMATE Scores |
| deconvo_ips | Calculate Immunophenoscore (IPS) |
| deconvolute_quantiseq.default | Use quanTIseq to Deconvolute a Gene Expression Matrix |
| deconvolute_timer.default | Deconvolute Tumor Microenvironment Using TIMER |
| deconvo_mcpcounter | Deconvolve Immune Microenvironment Using MCP-Counter |
| deconvo_quantiseq | Deconvolve Using quanTIseq |
| deconvo_ref | Deconvolve Using Custom Reference |
| deconvo_timer | Deconvolve Using TIMER |
| deconvo_tme | Main TME Deconvolution Function |
| deconvo_xcell | Deconvolve Immune Microenvironment Using xCell |
| design_mytheme | Design Custom Theme for ggplot2 Plots |
| doPerm | Permutation Test for CIBERSORT |
| dot-appendSignatures | Append Signatures to Expression Matrix |
| dot-build_mut_matrices | Build Mutation Matrices from MAF Data |
| dot-create_mut_matrix | Create Single Mutation Matrix |
| download_iobr_data | Download IOBR Data from GitHub with Mirror Support |
| DrawQQPlot | Draw QQ Plot Comparing Cancer and Immune Expression |
| Enet | Elastic Net Model Fitting |
| enrichment_barplot | Enrichment Bar Plot with Two Directions |
| EPIC | Estimate the proportion of immune and cancer cells. |
| eset_distribution | Visualize Expression Set Distribution |
| estimateScore | estimateScore |
| exact_pvalue | Calculate Exact P-Value for Correlation |
| extract_sc_data | Extract Data Frame from Seurat Object |
| feature_manipulation | Feature Quality Control and Filtering |
| feature_select | Feature Selection via Correlation or Differential Expression |
| filterCommonGenes | filterCommonGenes |
| find_markers_in_bulk | Identify Marker Features in Bulk Expression Data |
| find_mutations | Analyze Mutations Related to Signature Scores |
| find_outlier_samples | Identify Outlier Samples in Gene Expression Data |
| find_variable_genes | Identify Variable Genes in Expression Data |
| fixMixture | Fix Expression Mixture Matrix |
| format_msigdb | Format Input Signatures from MSigDB |
| format_signatures | Transform Signature Data into List Format |
| generateRef | Generate Reference Signature Matrix |
| generateRef_DEseq2 | Generate Reference Signature Matrix Using DESeq2 |
| generateRef_limma | Generate Reference Signature Matrix Using Limma |
| generateRef_rnaseq | Generate Reference Gene Matrix from RNA-seq DEGs |
| generateRef_seurat | Generate Reference Matrix from Seurat Object |
| get_cols | Set and View Color Palettes |
| get_cor | Calculate and Visualize Correlation Between Two Variables |
| get_cor_matrix | Calculate and Visualize Correlation Matrix Between Two... |
| get_default_mirrors | Get Default Download Mirrors |
| GetFractions.Abbas | Constrained Regression Method (Abbas et al., 2009) |
| getHRandCIfromCoxph | Extract Hazard Ratio and Confidence Intervals from Cox Model |
| get_iobr_cache_dir | Get IOBR Cache Directory |
| GetOutlierGenes | Get Outlier Genes |
| get_sig_sc | Extract Top Marker Genes from Single-Cell Differential... |
| gsva_use_new_api | GSVA API Version Detection |
| high_var_fea | Identify High-Variance Features from Statistical Results |
| imvigor210_pdata | IMvigor210 Bladder Cancer Immunotherapy Cohort Data |
| iobr_cor_plot | Integrative Correlation Analysis Between Phenotype and... |
| iobr_deconvo_pipeline | Tumor Microenvironment (TME) Deconvolution Pipeline |
| iobr_deg | Differential Expression Analysis |
| iobr_pca | Principal Component Analysis (PCA) Visualization |
| IPS_calculation | Calculate Immunophenoscore (IPS) |
| ipsmap | Map Score to Immunophenoscore |
| lasso_select | Feature Selection for Predictive or Prognostic Models Using... |
| limma.dif | Differential Expression Analysis Using Limma |
| list_github_datasets | List Available GitHub Datasets |
| list_iobr_mirrors | List Current Download Mirrors |
| load_data | Load IOBR Datasets |
| log2eset | Log2 Transformation of Gene Expression Matrix |
| LR_cal | Calculate Ligand-Receptor Interaction Scores |
| make_mut_matrix | Construct Mutation Matrices from MAF Data |
| makeQN | Quantile Normalization |
| mapbw | Map Score to Black and White Color |
| mapcolors | Map Score to Color |
| mapGenes | Map Gene Names to Approved Symbols |
| MCPcounter.estimate | MCP-counter Cell Population Abundance Estimation |
| merge_duplicate | Merge Data Frames with Duplicated Column Names |
| merge_duplicates | Merging the duplicates from the input matrix. |
| merge_eset | Merge Expression Sets by Row Names |
| microenvironmentScores | Calculate Microenvironment Scores |
| mouse2human_eset | Convert Mouse Gene Symbols to Human Gene Symbols |
| null_models | NULL Model Coefficients for MCPcounter |
| outputGCT | outputGCT |
| output_sig | Save Signature Data to File |
| palettes | Select Color Palettes for Visualization |
| parallel_doperm | Parallel Permutation Test for CIBERSORT |
| ParseInputExpression | Parse Input Gene Expression Data |
| patterns_to_na | Default Pattern List for Name Cleaning |
| pdata_stad | Toy STAD Phenotype Data |
| percent_bar_plot | Create a Percent Bar Plot |
| pie_chart | Create Pie or Donut Charts |
| PlotAUC | Plot AUC ROC Curves |
| plotPurity | plotPurity |
| PlotTimeROC | Plot Time-Dependent ROC Curves |
| ProcessingData | Process Data for Model Construction |
| PrognosticAUC | Calculate Time-Dependent AUC for Survival Models |
| PrognosticModel | Build Prognostic Models Using LASSO and Ridge Regression |
| PrognosticResult | Compute Prognostic Results for Survival Models |
| quanTIseq | Run quanTIseq Deconvolution |
| quantiseq_helper | Helper Functions for quanTIseq |
| random_strata_cells | Stratified Random Sampling of Cells |
| rawEnrichmentAnalysis | Calculate Raw xCell Enrichment Scores |
| rbind_iobr | Row Bind Multiple Data Sets |
| RegressionResult | Regression Result Computation |
| remove_batcheffect | Removing Batch Effect from Expression Sets |
| RemoveBatchEffect | Remove Batch Effect of Expression Set |
| remove_duplicate_genes | Remove Duplicate Gene Symbols in Gene Expression Data |
| remove_names | Remove Patterns from Column Names or Variables |
| reset_iobr_cache_dir | Reset IOBR Cache Directory to Default |
| reset_iobr_mirrors | Reset Download Mirrors to Default |
| roc_time | Time-dependent ROC Curve for Survival Analysis |
| scaleCounts | Scaling raw counts from each sample. |
| scale_matrix | Scale and Manipulate a Matrix |
| select_method | Select a Signature Scoring Method Subset |
| set_iobr_cache_dir | Set IOBR Cache Directory |
| sig_box | Signature Box Plot with Statistical Comparisons |
| sig_box_batch | Batch Signature Box Plots for Group Comparisons |
| sig_forest | Forest Plot for Survival Analysis Results |
| sig_group | Grouped gene signatures for IOBR analysis |
| sig_gsea | Perform Gene Set Enrichment Analysis (GSEA) |
| sig_heatmap | Signature Heatmap with Optional Annotations |
| signature_collection | Gene signature collection for pathway and immune analysis |
| signature_score_calculation_methods | Signature Score Calculation Methods |
| sig_pheatmap | Generate Heatmap for Signature Data |
| sig_roc | Plot ROC Curves and Compare Them |
| sigScore | Calculate Signature Score Using PCA, Mean, or Z-score Methods |
| sig_surv_plot | Generate Kaplan-Meier Survival Plot for Signature |
| spillOver | Adjust Scores Using Spillover Compensation |
| SplitTrainTest | Split Data into Training and Testing Sets |
| stad_group | Example Clinical Data for TCGA-STAD Gastric Cancer Analysis |
| subgroup_data | Example Dataset for Subgroup Survival Analysis |
| subgroup_survival | Subgroup Survival Analysis Using Cox Proportional Hazards... |
| surv_group | Generate Kaplan-Meier Survival Plots for Categorical Groups |
| tcga_rna_preps | Preprocess TCGA RNA-seq Data |
| tcga_stad_pdata | TCGA-STAD Clinical and Molecular Annotation Data |
| test_for_infiltration | Test for Cell Population Infiltration |
| timer_available_cancers | TIMER Available Cancer Types |
| timer_info | Source code for the TIMER deconvolution method. |
| tme_cluster | Identification of TME Cluster |
| tme_deconvolution_methods | TME Deconvolution Methods |
| Top_probe | Top Probe Selector |
| transform_data | Transform NA, Inf, or Zero Values in Data |
| transformScores | Transform Raw Scores to Fractions |
| xCellAnalysis | The xCell Analysis Pipeline |
| xCellSignifcanceBetaDist | Calculate Significance P-values Using Beta Distribution |
| xCellSignifcanceRandomMatrix | Calculate Significance Using Random Matrix |
