Interactive Analysis of UCSC Xena Data

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Documentation for package ‘UCSCXenaShiny’ version 2.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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
available_hosts	Show Available Hosts
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_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 dimension 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_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 dimension 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_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