NEWS

UCSCXenaShiny 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.

UCSCXenaShiny 2.2.1.9000

UCSCXenaShiny 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.

UCSCXenaShiny 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.

UCSCXenaShiny 2.1.0 (2024-05-15)

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

UCSCXenaShiny 2.0.1

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

UCSCXenaShiny 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")

UCSCXenaShiny 1.1.11

Fixed check warning in pan-cancer radar plot.

UCSCXenaShiny 1.1.10 (2023-02-28)

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

UCSCXenaShiny 1.1.9 (2022-12-12)

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

UCSCXenaShiny 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).

UCSCXenaShiny 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

UCSCXenaShiny 1.1.6

Added description of extra datasets.

UCSCXenaShiny 1.1.5 (2022-01-15)

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

UCSCXenaShiny 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.

UCSCXenaShiny 1.1.3 (2021-11-29)

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

UCSCXenaShiny 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.

UCSCXenaShiny 1.1.1 (2021-07-30)

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

UCSCXenaShiny 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.

UCSCXenaShiny 1.0.1 (2021-06-23)

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

UCSCXenaShiny 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.