UCSCXenaShiny 2.2.0-zenodo

Merge pull request #351 from lishensuo/master

Optimize some details

UCSCXenaShiny 2.1.0

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

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")

Release 1.1.10

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

Release 1.1.9

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

Release 1.1.8

UCSCXenaShiny 1.1.8

• 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).

Release 1.1.7

UCSCXenaShiny 1.1.7

• 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

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

Release 1.1.4

• 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.

Release 1.1.3

Latest docker image is available at https://hub.docker.com/r/shixiangwang/ucscxenashiny/tags/

Updates:

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

Committed and checked by Longfei, Yi Xiong and Shixiang.

Release 1.1.2

Latest docker image is available at https://hub.docker.com/r/shixiangwang/ucscxenashiny/tags/

UCSCXenaShiny 1.1.2

• 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

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