.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 |