BinomialAUC             Calculate AUC for Binomial Model
BinomialModel           Binomial Model Construction
CIBERSORT               CIBERSORT Deconvolution Algorithm
CalculatePref           Calculate Performance Metrics
CalculateTimeROC        Calculate Time-Dependent ROC Curve
Construct_con           Construct Contrast Matrix
ConvertRownameToLoci    Convert Rowname To Loci
CoreAlg                 Core Algorithm for CIBERSORT Deconvolution
DrawQQPlot              Draw QQ Plot Comparing Cancer and Immune
                        Expression
EPIC                    Estimate the proportion of immune and cancer
                        cells.
Enet                    Elastic Net Model Fitting
GetFractions.Abbas      Constrained Regression Method (Abbas et al.,
                        2009)
GetOutlierGenes         Get Outlier Genes
IPS_calculation         Calculate Immunophenoscore (IPS)
LR_cal                  Calculate Ligand-Receptor Interaction Scores
MCPcounter.estimate     MCP-counter Cell Population Abundance
                        Estimation
ParseInputExpression    Parse Input Gene Expression Data
PlotAUC                 Plot AUC ROC Curves
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
RegressionResult        Regression Result Computation
RemoveBatchEffect       Remove Batch Effect of Expression Set
SplitTrainTest          Split Data into Training and Testing Sets
Top_probe               Top Probe Selector
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
calculate_break_month   Break Time Into Blocks
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
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
clear_iobr_cache        Clear IOBR Data Cache
combine_pd_eset         Combine Phenotype Data and Expression Set
count2tpm               Convert Read Counts to Transcripts Per Million
                        (TPM)
creat_folder            Create Nested Output Folders
deconvo_cibersort       Deconvolve Using CIBERSORT
deconvo_epic            Deconvolve Immune Microenvironment Using EPIC
deconvo_estimate        Calculate ESTIMATE Scores
deconvo_ips             Calculate Immunophenoscore (IPS)
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
deconvolute_quantiseq.default
                        Use quanTIseq to Deconvolute a Gene Expression
                        Matrix
deconvolute_timer.default
                        Deconvolute Tumor Microenvironment Using TIMER
design_mytheme          Design Custom Theme for ggplot2 Plots
doPerm                  Permutation Test for CIBERSORT
download_iobr_data      Download IOBR Data from GitHub with Mirror
                        Support
enrichment_barplot      Enrichment Bar Plot with Two Directions
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
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
getHRandCIfromCoxph     Extract Hazard Ratio and Confidence Intervals
                        from Cox Model
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 Variable Sets
get_iobr_cache_dir      Get IOBR Cache Directory
get_sig_sc              Extract Top Marker Genes from Single-Cell
                        Differential Results
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 Features
iobr_deconvo_pipeline   Tumor Microenvironment (TME) Deconvolution
                        Pipeline
iobr_deg                Differential Expression Analysis
iobr_pca                Principal Component Analysis (PCA)
                        Visualization
ipsmap                  Map Score to Immunophenoscore
lasso_select            Feature Selection for Predictive or Prognostic
                        Models Using LASSO Regression
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
make_mut_matrix         Construct Mutation Matrices from MAF Data
mapbw                   Map Score to Black and White Color
mapcolors               Map Score to Color
merge_duplicate         Merge Data Frames with Duplicated Column Names
merge_eset              Merge Expression Sets by Row Names
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
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
plotPurity              plotPurity
random_strata_cells     Stratified Random Sampling of Cells
rbind_iobr              Row Bind Multiple Data Sets
remove_batcheffect      Removing Batch Effect from Expression Sets
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
scale_matrix            Scale and Manipulate a Matrix
select_method           Select a Signature Scoring Method Subset
set_iobr_cache_dir      Set IOBR Cache Directory
sigScore                Calculate Signature Score Using PCA, Mean, or
                        Z-score Methods
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
sig_pheatmap            Generate Heatmap for Signature Data
sig_roc                 Plot ROC Curves and Compare Them
sig_surv_plot           Generate Kaplan-Meier Survival Plot for
                        Signature
signature_collection    Gene signature collection for pathway and
                        immune analysis
signature_score_calculation_methods
                        Signature Score Calculation Methods
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 Models
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
transform_data          Transform NA, Inf, or Zero Values in Data
