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