đź“Š An R package for interactively exploring UCSC Xena https://xenabrowser.net/datapages/; Book: https://lishensuo.github.io/UCSCXenaShiny_Book; App online: https://shiny.hiplot.cn/ucsc-xena-shiny/, https://shiny.zhoulab.ac.cn/UCSCXenaShiny
See the UCSCXenaShiny v2 Book for a comprehensive guidance.
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..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 TypeHomepage
General Dataset Analysis
Quick TPC Analysis
Personalized Analysis
Download
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.
Test code:
vis_gene_tmb_cor("`ZFAT-AS1` + `SNORD116-1` + SPATA31D1", data_type = "methylation")
Fixed check issue due to internet access (#253).
include.Tumor.only
to control if include typeflatly
not available.ggsave()
failure in General Analysis page. (#230)as.data.frame()
when querying a symbol with unvalid R name. (Related to #234)Latest docker image is available at https://hub.docker.com/r/shixiangwang/ucscxenashiny/tags/
Updates:
ggsave()
failure. (#230)Committed and checked by Longfei, Yi Xiong and Shixiang.
Latest docker image is available at https://hub.docker.com/r/shixiangwang/ucscxenashiny/tags/
purrr
lambda function.This the first stable and formal version of UCSCXenaShiny
. We have refactored
the whole R package and corresponding Shiny for service.
Enjoy yourself.
This is the formal release of v1.0.0, the code is equal to the version submitted to CRAN.