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Changelog

Source: NEWS.md

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

CRAN release: 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

UCSCXenaShiny 2.0.0

CRAN release: 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"
)

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

CRAN release: 2023-02-28

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

UCSCXenaShiny 1.1.9

CRAN release: 2022-12-12

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

UCSCXenaShiny 1.1.8

CRAN release: 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

CRAN release: 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

CRAN release: 2022-01-15

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

UCSCXenaShiny 1.1.4

CRAN release: 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

CRAN release: 2021-11-29

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

UCSCXenaShiny 1.1.2

CRAN release: 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

CRAN release: 2021-07-30

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

UCSCXenaShiny 1.1.0

CRAN release: 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

CRAN release: 2021-06-23

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

UCSCXenaShiny 1.0.0

CRAN release: 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.