UCSCXenaShiny 2.0.0

See the UCSCXenaShiny v2 Book for a comprehensive guidance.

New Features

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.

.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

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.

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.

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")

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).

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

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.

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.

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.

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

Enjoy yourself.