UCSCXenaShiny 2.0.0

See the UCSCXenaShiny v2 Book for a comprehensive guidance.

New Features

Datasets

• load_data("tcga_PW"): ssGSEA scores of HALLMARK, KEGG, IOBR terms for TCGA samples.
• load_data("tcga_PW_meta"): metadata annotation for HALLMARK, KEGG, IOBR terms.
• load_data("pcawg_TIL"): PCAWG TIL data.
• load_data("pcawg_PW"): ssGSEA scores of HALLMARK, KEGG, IOBR terms for PCAWG samples.
• and more.

R Package Functions

• .opt_pancan : Default setting for alternative TPC datasets.
• mol_quick_analysis(): Quick molecule analysis and report generation based on TCGA dataset.
• query_tcga_group(): Group TPC samples by build-in or custom phenotype and support filtering or merging operations.
• vis_dim_dist(): Visualize the distribution difference of TCGA samples after dimension reduction analysis.
• vis_identifier_dim_dist(): Visualize the distribution difference of samples after Molecule Identifier dimension reduction analysis.
• 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

Shiny application

• Homepage

  • Added slicker gallery to display page summary;
  • Added report generation for TCGA pan-cancer exploration.

• General Dataset Analysis

  • Added one general dimension reduction analysis module.

• Quick TPC Analysis

  • Added one module for association analysis between molecule and pathway;
  • Added one module for association analysis between molecule and mutation;
  • Added one module for dimension reduction analysis.

• Personalized Analysis

  • Designed personalized TPC analysis pipelines for based on 3 methods and 3 modes.

• Download

  • Added two modules for exact subset of integrated TPC data and UCSCXena datasets.

Enhancements

• Supported getting more flexible methylation value.

UCSCXenaShiny::get_pancan_methylation_value(
  "RCAN2",
  rule_out = c("cg21115430", "cg19452802"), 
  aggr = "Q75"
)

• Supported installing the package from r-universe (https://openbiox.r-universe.dev/UCSCXenaShiny).

• Supported alternative molecular profiling datasets for quick and personalized TPC analysis.

Bug Fixes

• Merged data with unequal size in pan-cancer data query with a gene signature (#283), the fix also enhance the sample names match.

Test code:

vis_gene_tmb_cor("`ZFAT-AS1` + `SNORD116-1` + SPATA31D1", data_type = "methylation")