Changes in version 2.2.2                        

  - Added comprehensive gene and pathway cross-omics analysis for PCAWG
    and CCLE.
  - Standardized cross-omics visualization with TCGA standards (dynamic
    layouts, professional palettes).
  - Implemented flexible identifier selection (Transcript, CpG,
    Promoter, Antibody) in all cross-omics modules.
  - Added explicit 'Overall' median toggle to cross-omics analysis.
  - Resolved all dimension mismatch and logic errors in PCAWG/CCLE data
    joining.
  - Optimized remote data fetching with batch support and automatic
    retry logic.
  - Updated query_pancan_value() to support PCAWG mutation and improved
    robustness.
  - Fixed Specimen-to-Donor ID mapping for PCAWG mutation joins.

                     Changes in version 2.2.1.9000                      

                 Changes in version 2.2.1 (2026-05-05)                  

  - Added get_nonomics_value() function to fetch non-omics data.
  - Renamed quick analysis modules & Update README.
  - Added package logo.
  - Removed hiplot mirror switch from global settings.

                 Changes in version 2.2.0 (2025-08-01)                  

  - Adapted interleave().
  - Added gene and pathway cross-omics analysis functions/modules.
  - Added app_run2() function for custom app start with lightweight
    modules.
  - Fixed pdf() parameter for KM plot
  - Improved the UI of Custom TPC Modules.
  - Removed a mistake by Yi Xiong for setting problematic threshold
    parameter in unicox analysis.

                 Changes in version 2.1.0 (2024-05-15)                  

  - Handled error raised due to internet issue in CRAN check.
  - Optimized data preloading of Shiny application.
  - Dockerfile updated.

                        Changes in version 2.0.1                        

  - Fixed some minor bugs in Shiny app.
  - Updated README about Docker usage.
  - Fixed an issue in vis_identifier_grp_comparison() (#317).

                 Changes in version 2.0.0 (2024-03-14)                  

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 dimensionality reduction analysis.
  - vis_identifier_dim_dist(): Visualize the distribution difference of
    samples after Molecule Identifier dimensionality 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 dimensionality 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 dimensionality 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")

                       Changes in version 1.1.11                        

  - Fixed check warning in pan-cancer radar plot.

                 Changes in version 1.1.10 (2023-02-28)                 

  - Fixed check issue due to internet access (#253).

                 Changes in version 1.1.9 (2022-12-12)                  

  - Added cancer type control for PCAWG survival analysis.
  - Added TCGA batch id from MDA.

                 Changes in version 1.1.8 (2022-06-07)                  

  - Fixed issue to set mislabelled color in pcawg pan-cancer analysis
    (#247, Thanks to Tangjian Li).
  - Fixed issue in querying gene signature in general analysis page
    (#244).
  - Fixed issue "Radar plot “stemness” does not plot the “ACC” tumor
    type" (#242).

                 Changes in version 1.1.7 (2022-04-13)                  

  - Added option include.Tumor.only to control if include type
  - Set default theme if flatly not available.
  - Added example to generate radar plot, close #239

                        Changes in version 1.1.6                        

  - Added description of extra datasets.

                 Changes in version 1.1.5 (2022-01-15)                  

  - Fixed survival KM plot output issue due to ggsave() failure in
    General Analysis page. (#230)

                 Changes in version 1.1.4 (2021-12-13)                  

  - Fixed the colnames being changed by as.data.frame() when querying a
    symbol with unvalid R name. (Related to #234)
  - Added more informative error for scatter plot in General Analysis
    tab. (#233)
  - Reversed default color setting for groups in survival analysis to
    fit conventional color grouping (in Xena). (#232, thanks to feedback
    from Enrique)
  - Supported known science palette and custom colors for survival
    analysis in Quick PanCan Analysis tab.

                 Changes in version 1.1.3 (2021-11-29)                  

  - Data check. (#225)
  - Fixed survival KM plot output issue due to ggsave() failure. (#230)

                 Changes in version 1.1.2 (2021-11-17)                  

  - Fixed value query for gene signature with purrr lambda function.
  - Updated dataset doc.
  - Uploaded zenodo link.
  - Uploaded this tool to conda forge, the user can install it from
    conda now. For more details, please read the README file.

                 Changes in version 1.1.1 (2021-07-30)                  

  - Updated citation.
  - Fixed the data loading bug due to function scope problem (#222).

                 Changes in version 1.1.0 (2021-07-16)                  

  - Supported uploading data files for analysis.
  - Improved user experience.
  - Added more contents in README.
  - Corrected LICENSE (this package is built on the top of code with
    GPLv3 LICENCE).
  - Added docker image for UCSCXenaShiny
    https://hub.docker.com/r/shixiangwang/ucscxenashiny.

                 Changes in version 1.0.1 (2021-06-23)                  

  - Added a package doc site link in usage navbar list.
  - Fixed bug of PCAWG survival analysis (#209).

                 Changes in version 1.0.0 (2021-05-16)                  

This the first stable and formal version of UCSCXenaShiny. We have
refactored the whole R package and corresponding Shiny for service.

Enjoy yourself.