NEWS

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UCSCXenaShiny 2.2.0

• 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.