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

ccle_absolute

ABSOLUTE Result of CCLE Database

ccle_info

Phenotype Info of CCLE Database

toil_info

Toil Hub: TCGA TARGET GTEX Selected Phenotype

pcawg_info

Phenotype Info of PCAWG Database

pcawg_purity

Purity Data of PCAWG

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.

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

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

query_toil_value_df() query_toil_value_df()

Obtain ToilHub Info for Single Molecule

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_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_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

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

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

Shiny App

Functions related to Xena Shiny App

app_run()

Run UCSC Xena Shiny App

Others

Other docs

UCSCXenaShiny

Xena Shiny App

keep_cat_cols()

Keep Only Columns Used for Sample Selection