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Releases: openbiox/UCSCXenaShiny

UCSCXenaShiny 2.2.0-zenodo

26 Aug 04:10
29d0b16
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Merge pull request #351 from lishensuo/master

Optimize some details

UCSCXenaShiny 2.1.0

15 May 16:42
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  • Handled error raised due to internet issue in CRAN check and tests.
  • Optimized data preloading of Shiny application.
  • Dockerfile updated.

UCSCXenaShiny 2.0.0

14 Mar 04:58
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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"
)

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

23 Apr 02:59
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Fixed check issue due to internet access (#253).

Release 1.1.9

08 Dec 13:19
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  • Added cancer type control for PCAWG survival analysis.
  • Added TCGA batch id from MDA.

Release 1.1.8

07 Jun 14:19
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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

13 Apr 08:41
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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

13 Dec 04:02
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  • 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

29 Nov 04:07
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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

17 Nov 05:40
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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).