Man pages for UCSCXenaShiny
Interactive Analysis of UCSC Xena Data
| analyze_gene_drug_response_asso | Analyze Association between Gene (Signature) and Drug... |
| analyze_gene_drug_response_diff | Analyze Difference of Drug Response (IC50 Value (uM)) between... |
| 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 |
| dot-opt_pancan | A default setting for pan-cancer studies |
| ezcor | Run Correlation between Two Variables and Support Group by a... |
| ezcor_batch | Run correlation between two variables in a batch mode and... |
| ezcor_partial_cor | Run partial correlation |
| get_pancan_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 |
| pipe | Pipe Operator |
| query_general_value | download data for shiny general analysis |
| query_molecule_value | Get Molecule or Signature Data Values from Dense (Genomic)... |
| query_pancan_value | Query Single Identifier or Signature Value from Pan-cancer... |
| query_tcga_group | Group TPC samples by build-in or custom phenotype and support... |
| query_toil_value_df | Obtain ToilHub Info for Single Molecule |
| 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.organ | TCGA: Organ Data |
| tcga_purity | TCGA: Purity Data |
| tcga_subtypes | TCGA Subtype Data |
| tcga_surv | Toil Hub: TCGA Survival Data |
| tcga_surv_analysis | TCGA Survival Analysis |
| tcga_tmb | TCGA: TMB (Tumor Mutation Burden) Data |
| toil_info | Toil Hub: TCGA TARGET GTEX Selected Phenotype |
| UCSCXenaShiny-package | Xena Shiny App |
| 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... |
| 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... |
| vis_gene_pw_cor | Visualize Correlation between Gene and Pathway signature... |
| vis_gene_stemness_cor | Visualize Correlation between Gene and Tumor Stemness |
| vis_gene_TIL_cor | Heatmap for Correlation between Gene and Tumor Immune... |
| vis_gene_tmb_cor | Visualize Correlation between Gene and TMB (Tumor Mutation... |
| vis_identifier_cor | Visualize Identifier-Identifier Correlation |
| vis_identifier_dim_dist | Visualize the distribution difference of samples after... |
| 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... |
| vis_toil_Mut_cancer | Visualize molecular profile difference between mutation and... |
| vis_toil_TvsN | Visualize Pan-cancer TPM (tumor (TCGA) vs Normal (TCGA &... |
| vis_toil_TvsN_cancer | Visualize Gene TPM in Single Cancer Type (Tumor (TCGA) vs... |
| vis_unicox_tree | Visualize Single Gene Univariable Cox Result from Toil Data... |
