Tutorial Book | Fetch Data | Fetch Gene Expression | Fetch Transcript Expression | Fetch Gene CNV | Fetch Gene Mutation | Fetch miRNA mature strand expression | Data Visualization | Visualize Single Gene Expression in PANCAN Dataset | Compare Gene Expression Level in Single Cancer Type | Compare Gene Expression Level in Different Anatomic Regions | Visualize Relationship between Gene Expression and Prognosis in the PANCAN Dataset | Other Functions and Data
Package: UCSCXenaShiny 2.2.1.9000
Shixiang Wang
UCSCXenaShiny: Interactive Analysis of UCSC Xena Data
Provides functions and a Shiny application for downloading, analyzing and visualizing datasets from UCSC Xena (<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Authors:
UCSCXenaShiny_2.2.1.9000.tar.gz
UCSCXenaShiny_2.2.1.9000.zip(r-4.7)UCSCXenaShiny_2.2.1.9000.zip(r-4.6)UCSCXenaShiny_2.2.1.9000.zip(r-4.5)
UCSCXenaShiny_2.2.1.9000.tgz(r-4.6-any)UCSCXenaShiny_2.2.1.9000.tgz(r-4.5-any)
UCSCXenaShiny_2.2.1.9000.tar.gz(r-4.7-any)UCSCXenaShiny_2.2.1.9000.tar.gz(r-4.6-any)
UCSCXenaShiny_2.2.1.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
UCSCXenaShiny/json (API)
| # Install 'UCSCXenaShiny' in R: |
| install.packages('UCSCXenaShiny', repos = c('https://openbiox.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/openbiox/ucscxenashiny/issues
Pkgdown/docs site:https://openbiox.github.io
Datasets:
- ccle_absolute - ABSOLUTE Result of CCLE Database
- ccle_info - Phenotype Info of CCLE Database
- ccle_info_fine - Cleaned Phenotype Info of CCLE Database for grouping
- pcawg_info - Phenotype Info of PCAWG Database
- pcawg_info_fine - Cleaned Phenotype Info of PCAWG Database for grouping
- pcawg_purity - Purity Data of PCAWG
- tcga_clinical - Toil Hub: TCGA Clinical Data
- tcga_clinical_fine - Toil Hub: Cleaned TCGA Clinical Data for grouping
- tcga_genome_instability - TCGA: Genome Instability Data
- tcga_gtex - Toil Hub: Merged TCGA GTEx Selected Phenotype
- tcga_purity - TCGA: Purity Data
- tcga_subtypes - TCGA Subtype Data
- tcga_surv - Toil Hub: TCGA Survival Data
- TCGA.organ - TCGA: Organ Data
- toil_info - Toil Hub: TCGA TARGET GTEX Selected Phenotype
cancer-datasetshiny-appsucsc-xena
Last updated from:e012e4a3e7. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 225 | ||
| source / vignettes | OK | 365 | ||
| linux-release-x86_64 | OK | 216 | ||
| macos-release-arm64 | OK | 180 | ||
| macos-oldrel-arm64 | OK | 188 | ||
| windows-devel | OK | 145 | ||
| windows-release | OK | 138 | ||
| windows-oldrel | OK | 137 | ||
| wasm-release | OK | 159 |
Exports:.opt_pancan%>%analyze_gene_drug_response_assoanalyze_gene_drug_response_diffapp_runapp_run2available_hostsezcorezcor_batchezcor_partial_corget_ccle_cn_valueget_ccle_gene_valueget_ccle_mutation_statusget_ccle_protein_valueget_nonomics_valueget_pancan_cn_valueget_pancan_gene_valueget_pancan_methylation_valueget_pancan_miRNA_valueget_pancan_mutation_statusget_pancan_protein_valueget_pancan_transcript_valueget_pancan_valueget_pcawg_APOBEC_mutagenesis_valueget_pcawg_cn_valueget_pcawg_fusion_valueget_pcawg_gene_valueget_pcawg_miRNA_valueget_pcawg_mutation_statusget_pcawg_promoter_valuekeep_cat_colsload_datamol_quick_analysisquery_molecule_valuequery_pancan_valuequery_tcga_groupquery_toil_value_dftcga_surv_gettcga_surv_plotvis_ccle_gene_corvis_ccle_gene_cross_omicsvis_ccle_tpmvis_dim_distvis_gene_corvis_gene_cor_cancervis_gene_cross_omicsvis_gene_drug_response_assovis_gene_drug_response_diffvis_gene_immune_corvis_gene_msi_corvis_gene_pw_corvis_gene_stemness_corvis_gene_TIL_corvis_gene_tmb_corvis_identifier_corvis_identifier_dim_distvis_identifier_grp_comparisonvis_identifier_grp_survvis_identifier_multi_corvis_pancan_anatomyvis_pcawg_distvis_pcawg_gene_corvis_pcawg_gene_cross_omicsvis_pcawg_pathway_cross_omicsvis_pcawg_unicox_treevis_toil_Mutvis_toil_Mut_cancervis_toil_TvsNvis_toil_TvsN_cancervis_unicox_tree
Dependencies:abindaskpassbackportsbase64encbitbit64bootbroombslibcachemcarcarDataclicliprcolorspacecommonmarkcorrplotcowplotcpp11crayoncurlDerivdigestdoBydplyrezcoxfarverfastmapfontawesomeforcatsforecastforestmodelFormulafracdifffsgenericsggplot2ggpubrggrepelggsciggsignifglueGPArotationgridExtragtablehmshtmltoolshttpuvhttrisobandjquerylibjsonlitelabelinglaterlatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamnormtmodelrnlmenloptrnnetnumDerivopensslotelpbkrtestpillarpkgconfigpolynomppcorprettyunitsprogresspromisespsychpurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreformulasrlangrstatixS7sassscalesshinysourcetoolsSparseMstringistringrsurvivalsystibbletidyrtidyselecttimeDatetzdbUCSCXenaToolsurcautf8vctrsviridisLitevroomwithrxtablezoo
