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Data

Builtin datasets and functions to load data

load_data()
Load Dataset Provided by This Package
TCGA.organ
TCGA: Organ Data
tcga_clinical
Toil Hub: TCGA Clinical Data
tcga_surv
Toil Hub: TCGA Survival Data
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_tmb
TCGA: TMB (Tumor Mutation Burden) Data
tcga_clinical_fine
Toil Hub: Cleaned TCGA Clinical Data for grouping
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
toil_info
Toil Hub: TCGA TARGET GTEX Selected Phenotype
pcawg_info
Phenotype Info of PCAWG Database
pcawg_purity
Purity Data of PCAWG
pcawg_info_fine
Cleaned Phenotype Info of PCAWG Database for grouping

Data Query

Functions to query data from UCSC Xena data hubs in single molecular level. The functionality of functions below may overlap, we rank them by importance.

.opt_pancan
A default setting for pan-cancer studies
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_general_value()
Download data for shiny general analysis
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
get_ccle_cn_value() get_ccle_gene_value() get_ccle_protein_value() get_ccle_mutation_status() get_pancan_value() get_pancan_gene_value() get_pancan_transcript_value() get_pancan_protein_value() get_pancan_mutation_status() get_pancan_cn_value() get_pancan_methylation_value() get_pancan_miRNA_value() get_pcawg_gene_value() get_pcawg_fusion_value() get_pcawg_promoter_value() get_pcawg_miRNA_value() get_pcawg_APOBEC_mutagenesis_value()
Fetch Identifier Value from Pan-cancer Dataset
available_hosts()
Show Available Hosts

Analysis and Visualiation for Pan-Cancer Study

Functions to analyze and visualize data mainly from TCGA, PCAWG and CCLE

tcga_surv_get() tcga_surv_plot()
TCGA Survival Analysis
analyze_gene_drug_response_asso()
Analyze Association between Gene (Signature) and Drug Response with CCLE Data
vis_gene_drug_response_asso()
Visualize Gene and Drug-Target Association 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
vis_gene_drug_response_diff()
Visualize Gene and Drug Response Difference with CCLE Data
vis_ccle_tpm()
Visualize CCLE Gene Expression
vis_ccle_gene_cor()
Visualize CCLE Gene Expression Correlation
vis_gene_TIL_cor()
Heatmap for Correlation between Gene and Tumor Immune Infiltration (TIL)
vis_gene_immune_cor()
Heatmap for Correlation between Gene and Immune Signatures
vis_gene_cor()
Visualize Gene-Gene Correlation in TCGA
vis_gene_cor_cancer()
Visualize Gene-Gene Correlation in a TCGA Cancer Type
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_gene_msi_cor()
Visualize Correlation between Gene and MSI (Microsatellite instability)
vis_gene_pw_cor()
Visualize Correlation between Gene and Pathway signature Score
vis_pancan_anatomy()
Visualize Single Gene Expression in Anatomy Location
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_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_unicox_tree()
Visualize Single Gene Univariable Cox Result from Toil Data Hub
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_gene_cross_omics()
Visualize cross-omics of one gene among pan-cancers
vis_pathway_cross_omics()
Visualize cross-omics of one pathway among pan-cancers
calc_pw_mut_cnv()
Prepare Mut/CNV data of pathways given specific samples

General Analysis and Visualiation

Functions to analyze and visualize general data, i.e., any valid data from UCSC Xena or users

vis_identifier_cor()
Visualize Identifier-Identifier Correlation
vis_identifier_multi_cor()
Visualize Correlation for Multiple Identifiers
vis_identifier_grp_comparison()
Visualize Comparison of an Molecule Identifier between Groups
vis_identifier_grp_surv()
Visualize Identifier Group Survival Difference
vis_dim_dist()
Visualize the distribution difference of samples after dimensionality reduction analysis
vis_identifier_dim_dist()
Visualize the distribution difference of samples after Molecule Identifier dimensionality reduction analysis
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

EDA & Report

Functions for exploratory data analysis and report.

mol_quick_analysis()
Quick molecule analysis and report generation

Shiny App

Functions related to Xena Shiny App

app_run()
Run UCSC Xena Shiny App
app_run2()
Run UCSC Xena Shiny App with specifc content

Others

Other docs

UCSCXenaShiny UCSCXenaShiny-package
Xena Shiny App
keep_cat_cols()
Keep Only Columns Used for Sample Selection