# Interactive Analysis of UCSC Xena Data

## Documentation for package ‘UCSCXenaShiny’ version 2.2.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

.opt_pancan | A default setting for pan-cancer studies
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_ccle_gene_value | Fetch Identifier Value from Pan-cancer Dataset
get_ccle_mutation_status | Fetch Identifier Value from Pan-cancer Dataset
get_ccle_protein_value | Fetch Identifier Value from Pan-cancer Dataset
get_nonomics_value | Fetch non-omics data of all samples from relevant databases
get_pancan_cn_value | Fetch Identifier Value from Pan-cancer Dataset
get_pancan_gene_value | Fetch Identifier Value from Pan-cancer Dataset
get_pancan_methylation_value | Fetch Identifier Value from Pan-cancer Dataset
get_pancan_miRNA_value | Fetch Identifier Value from Pan-cancer Dataset
get_pancan_mutation_status | Fetch Identifier Value from Pan-cancer Dataset
get_pancan_protein_value | Fetch Identifier Value from Pan-cancer Dataset
get_pancan_transcript_value | Fetch Identifier Value from Pan-cancer Dataset
get_pancan_value | Fetch Identifier Value from Pan-cancer Dataset
get_pcawg_APOBEC_mutagenesis_value | Fetch Identifier Value from Pan-cancer Dataset
get_pcawg_fusion_value | Fetch Identifier Value from Pan-cancer Dataset
get_pcawg_gene_value | Fetch Identifier Value from Pan-cancer Dataset
get_pcawg_miRNA_value | Fetch Identifier Value from Pan-cancer Dataset
get_pcawg_promoter_value | Fetch Identifier Value from Pan-cancer Dataset
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.organ | TCGA: Organ Data
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_surv_get | TCGA Survival Analysis
tcga_surv_plot | TCGA Survival Analysis
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_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_TIL_cor | Heatmap for Correlation between Gene and Tumor Immune Infiltration (TIL)
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