.opt_pancan             A default setting for pan-cancer studies
TCGA.organ              TCGA: Organ Data
analyze_gene_drug_response_asso
                        Analyze Association between Gene (Signature)
                        and Drug Response with CCLE Data
analyze_gene_drug_response_diff
                        Analyze Difference of Drug Response (IC50 Value
                        (uM)) between Gene (Signature) High and Low
                        Expression with CCLE Data
app_run                 Run UCSC Xena Shiny App
app_run2                Run UCSC Xena Shiny App with specifc content
available_hosts         Show Available Hosts
calc_pw_mut_cnv         Prepare Mut/CNV data of pathways given specific
                        samples
ccle_absolute           ABSOLUTE Result of CCLE Database
ccle_info               Phenotype Info of CCLE Database
ccle_info_fine          Cleaned Phenotype Info of CCLE Database for
                        grouping
ezcor                   Run Correlation between Two Variables and
                        Support Group by a Variable
ezcor_batch             Run correlation between two variables in a
                        batch mode and support group by a variable
ezcor_partial_cor       Run partial correlation
get_ccle_cn_value       Fetch Identifier Value from Pan-cancer Dataset
get_nonomics_value      Fetch non-omics data of all samples from
                        relevant databases
keep_cat_cols           Keep Only Columns Used for Sample Selection
load_data               Load Dataset Provided by This Package
mol_quick_analysis      Quick molecule analysis and report generation
pcawg_info              Phenotype Info of PCAWG Database
pcawg_info_fine         Cleaned Phenotype Info of PCAWG Database for
                        grouping
pcawg_purity            Purity Data of PCAWG
query_general_value     Download data for shiny general analysis
query_molecule_value    Get Molecule or Signature Data Values from
                        Dense (Genomic) Matrix Dataset of UCSC Xena
                        Data Hubs
query_pancan_value      Query Single Identifier or Signature Value from
                        Pan-cancer Database
query_tcga_group        Group TPC samples by build-in or custom
                        phenotype and support filtering or merging
                        operations
query_toil_value_df     Obtain ToilHub Info for Single Molecule
tcga survival analysis
                        TCGA Survival Analysis
tcga_clinical           Toil Hub: TCGA Clinical Data
tcga_clinical_fine      Toil Hub: Cleaned TCGA Clinical Data for
                        grouping
tcga_genome_instability
                        TCGA: Genome Instability Data
tcga_gtex               Toil Hub: Merged TCGA GTEx Selected Phenotype
tcga_purity             TCGA: Purity Data
tcga_subtypes           TCGA Subtype Data
tcga_surv               Toil Hub: TCGA Survival Data
tcga_tmb                TCGA: TMB (Tumor Mutation Burden) Data
toil_info               Toil Hub: TCGA TARGET GTEX Selected Phenotype
vis_ccle_gene_cor       Visualize CCLE Gene Expression Correlation
vis_ccle_tpm            Visualize CCLE Gene Expression
vis_dim_dist            Visualize the distribution difference of
                        samples after dimensionality reduction analysis
vis_gene_TIL_cor        Heatmap for Correlation between Gene and Tumor
                        Immune Infiltration (TIL)
vis_gene_cor            Visualize Gene-Gene Correlation in TCGA
vis_gene_cor_cancer     Visualize Gene-Gene Correlation in a TCGA
                        Cancer Type
vis_gene_cross_omics    Visualize cross-omics of one gene among
                        pan-cancers
vis_gene_drug_response_asso
                        Visualize Gene and Drug-Target Association with
                        CCLE Data
vis_gene_drug_response_diff
                        Visualize Gene and Drug Response Difference
                        with CCLE Data
vis_gene_immune_cor     Heatmap for Correlation between Gene and Immune
                        Signatures
vis_gene_msi_cor        Visualize Correlation between Gene and MSI
                        (Microsatellite instability)
vis_gene_pw_cor         Visualize Correlation between Gene and Pathway
                        signature Score
vis_gene_stemness_cor   Visualize Correlation between Gene and Tumor
                        Stemness
vis_gene_tmb_cor        Visualize Correlation between Gene and TMB
                        (Tumor Mutation Burden)
vis_identifier_cor      Visualize Identifier-Identifier Correlation
vis_identifier_dim_dist
                        Visualize the distribution difference of
                        samples after Molecule Identifier
                        dimensionality reduction analysis
vis_identifier_grp_comparison
                        Visualize Comparison of an Molecule Identifier
                        between Groups
vis_identifier_grp_surv
                        Visualize Identifier Group Survival Difference
vis_identifier_multi_cor
                        Visualize Correlation for Multiple Identifiers
vis_pancan_anatomy      Visualize Single Gene Expression in Anatomy
                        Location
vis_pathway_cross_omics
                        Visualize cross-omics of one pathway among
                        pan-cancers
vis_pcawg_dist          Visualize molecular profile in PCAWG
vis_pcawg_gene_cor      Visualize Gene-Gene Correlation in TCGA
vis_pcawg_unicox_tree   Visualize Single Gene Univariable Cox Result in
                        PCAWG
vis_toil_Mut            Visualize molecular profile difference between
                        mutation and wild status of queried gene
vis_toil_Mut_cancer     Visualize molecular profile difference between
                        mutation and wild status of queried gene in
                        Single Cancer Type
vis_toil_TvsN           Visualize Pan-cancer TPM (tumor (TCGA) vs
                        Normal (TCGA & GTEx))
vis_toil_TvsN_cancer    Visualize Gene TPM in Single Cancer Type (Tumor
                        (TCGA) vs Normal (TCGA & GTEx))
vis_unicox_tree         Visualize Single Gene Univariable Cox Result
                        from Toil Data Hub
