Package: UCSCXenaShiny 2.2.0

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:Shixiang Wang [aut, cre], Shensuo Li [aut], Yi Xiong [aut], Longfei Zhao [aut], Kai Gu [aut], Yin Li [aut], Fei Zhao [aut]

UCSCXenaShiny_2.2.0.tar.gz
UCSCXenaShiny_2.2.0.zip(r-4.5)UCSCXenaShiny_2.2.0.zip(r-4.4)UCSCXenaShiny_2.2.0.zip(r-4.3)
UCSCXenaShiny_2.2.0.tgz(r-4.4-any)UCSCXenaShiny_2.2.0.tgz(r-4.3-any)
UCSCXenaShiny_2.2.0.tar.gz(r-4.5-noble)UCSCXenaShiny_2.2.0.tar.gz(r-4.4-noble)
UCSCXenaShiny_2.2.0.tgz(r-4.4-emscripten)UCSCXenaShiny_2.2.0.tgz(r-4.3-emscripten)
UCSCXenaShiny.pdf |UCSCXenaShiny.html✨
UCSCXenaShiny/json (API)
NEWS

# Install 'UCSCXenaShiny' in R:
install.packages('UCSCXenaShiny', repos = c('https://shixiangwang.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/openbiox/ucscxenashiny/issues

Datasets:

On CRAN:

cancer-datasetshiny-appsucsc-xena

8.66 score 94 stars 34 scripts 406 downloads 66 exports 112 dependencies

Last updated 16 days agofrom:4f4e359aa9. Checks:OK: 7. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-winOKNov 06 2024
R-4.5-linuxOKNov 06 2024
R-4.4-winOKNov 06 2024
R-4.4-macOKNov 06 2024
R-4.3-winOKNov 06 2024
R-4.3-macOKNov 06 2024

Exports:.opt_pancan%>%analyze_gene_drug_response_assoanalyze_gene_drug_response_diffapp_runapp_run2available_hostscalc_pw_mut_cnvezcorezcor_batchezcor_partial_corget_ccle_cn_valueget_ccle_gene_valueget_ccle_mutation_statusget_ccle_protein_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_fusion_valueget_pcawg_gene_valueget_pcawg_miRNA_valueget_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_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_pathway_cross_omicsvis_pcawg_distvis_pcawg_gene_corvis_pcawg_unicox_treevis_toil_Mutvis_toil_Mut_cancervis_toil_TvsNvis_toil_TvsN_cancervis_unicox_tree

Dependencies:abindaskpassbackportsbase64encbitbit64bootbroombslibcachemcarcarDataclicliprcolorspacecommonmarkcorrplotcowplotcpp11crayoncurlDerivdigestdoBydplyrezcoxfansifarverfastmapfontawesomeforcatsforestmodelFormulafsgenericsggplot2ggpubrggrepelggsciggsignifglueGPArotationgridExtragtablehmshtmltoolshttpuvhttrisobandjquerylibjsonlitelabelinglaterlatticelifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamnormtmodelrmunsellnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigpolynomppcorprettyunitsprogresspromisespsychpurrrquantregR6rappdirsRColorBrewerRcppRcppEigenreadrrlangrstatixsassscalesshinysourcetoolsSparseMstringistringrsurvivalsystibbletidyrtidyselecttzdbUCSCXenaToolsutf8vctrsviridisLitevroomwithrxtable

Examples of Accessible Functions

Shixiang Wang, Yi Xiong, Longfei Zhao, Kai Gu, Yin Li, Fei Zhao

Rendered fromapi.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-07-18
Started: 2021-03-26

Readme and manuals

Help Manual

Help pageTopics
A default setting for pan-cancer studies.opt_pancan
Analyze Association between Gene (Signature) and Drug Response with CCLE Dataanalyze_gene_drug_response_asso
Analyze Difference of Drug Response (IC50 Value (uM)) between Gene (Signature) High and Low Expression with CCLE Dataanalyze_gene_drug_response_diff
Run UCSC Xena Shiny Appapp_run
Run UCSC Xena Shiny App with specifc contentapp_run2
Show Available Hostsavailable_hosts
Prepare Mut/CNV data of pathways given specific samplescalc_pw_mut_cnv
ABSOLUTE Result of CCLE Databaseccle_absolute
Phenotype Info of CCLE Databaseccle_info
Cleaned Phenotype Info of CCLE Database for groupingccle_info_fine
Run Correlation between Two Variables and Support Group by a Variableezcor
Run correlation between two variables in a batch mode and support group by a variableezcor_batch
Run partial correlationezcor_partial_cor
Fetch Identifier Value from Pan-cancer Datasetget_ccle_cn_value get_ccle_gene_value get_ccle_mutation_status get_ccle_protein_value get_pancan_cn_value get_pancan_gene_value get_pancan_methylation_value get_pancan_miRNA_value get_pancan_mutation_status get_pancan_protein_value get_pancan_transcript_value get_pancan_value get_pcawg_APOBEC_mutagenesis_value get_pcawg_fusion_value get_pcawg_gene_value get_pcawg_miRNA_value get_pcawg_promoter_value
Keep Only Columns Used for Sample Selectionkeep_cat_cols
Load Dataset Provided by This Packageload_data
Quick molecule analysis and report generationmol_quick_analysis
Phenotype Info of PCAWG Databasepcawg_info
Cleaned Phenotype Info of PCAWG Database for groupingpcawg_info_fine
Purity Data of PCAWGpcawg_purity
Download data for shiny general analysisquery_general_value
Get Molecule or Signature Data Values from Dense (Genomic) Matrix Dataset of UCSC Xena Data Hubsquery_molecule_value
Query Single Identifier or Signature Value from Pan-cancer Databasequery_pancan_value
Group TPC samples by build-in or custom phenotype and support filtering or merging operationsquery_tcga_group
Obtain ToilHub Info for Single Moleculequery_toil_value_df
TCGA Survival Analysistcga survival analysis tcga_surv_get tcga_surv_plot
Toil Hub: TCGA Clinical Datatcga_clinical
Toil Hub: Cleaned TCGA Clinical Data for groupingtcga_clinical_fine
TCGA: Genome Instability Datatcga_genome_instability
Toil Hub: Merged TCGA GTEx Selected Phenotypetcga_gtex
TCGA: Purity Datatcga_purity
TCGA Subtype Datatcga_subtypes
Toil Hub: TCGA Survival Datatcga_surv
TCGA: TMB (Tumor Mutation Burden) Datatcga_tmb
TCGA: Organ DataTCGA.organ
Toil Hub: TCGA TARGET GTEX Selected Phenotypetoil_info
Visualize CCLE Gene Expression Correlationvis_ccle_gene_cor
Visualize CCLE Gene Expressionvis_ccle_tpm
Visualize the distribution difference of samples after dimensionality reduction analysisvis_dim_dist
Visualize Gene-Gene Correlation in TCGAvis_gene_cor
Visualize Gene-Gene Correlation in a TCGA Cancer Typevis_gene_cor_cancer
Visualize cross-omics of one gene among pan-cancersvis_gene_cross_omics
Visualize Gene and Drug-Target Association with CCLE Datavis_gene_drug_response_asso
Visualize Gene and Drug Response Difference with CCLE Datavis_gene_drug_response_diff
Heatmap for Correlation between Gene and Immune Signaturesvis_gene_immune_cor
Visualize Correlation between Gene and MSI (Microsatellite instability)vis_gene_msi_cor
Visualize Correlation between Gene and Pathway signature Scorevis_gene_pw_cor
Visualize Correlation between Gene and Tumor Stemnessvis_gene_stemness_cor
Heatmap for Correlation between Gene and Tumor Immune Infiltration (TIL)vis_gene_TIL_cor
Visualize Correlation between Gene and TMB (Tumor Mutation Burden)vis_gene_tmb_cor
Visualize Identifier-Identifier Correlationvis_identifier_cor
Visualize the distribution difference of samples after Molecule Identifier dimensionality reduction analysisvis_identifier_dim_dist
Visualize Comparison of an Molecule Identifier between Groupsvis_identifier_grp_comparison
Visualize Identifier Group Survival Differencevis_identifier_grp_surv
Visualize Correlation for Multiple Identifiersvis_identifier_multi_cor
Visualize Single Gene Expression in Anatomy Locationvis_pancan_anatomy
Visualize cross-omics of one pathway among pan-cancersvis_pathway_cross_omics
Visualize molecular profile in PCAWGvis_pcawg_dist
Visualize Gene-Gene Correlation in TCGAvis_pcawg_gene_cor
Visualize Single Gene Univariable Cox Result in PCAWGvis_pcawg_unicox_tree
Visualize molecular profile difference between mutation and wild status of queried genevis_toil_Mut
Visualize molecular profile difference between mutation and wild status of queried gene in Single Cancer Typevis_toil_Mut_cancer
Visualize Pan-cancer TPM (tumor (TCGA) vs Normal (TCGA & GTEx))vis_toil_TvsN
Visualize Gene TPM in Single Cancer Type (Tumor (TCGA) vs Normal (TCGA & GTEx))vis_toil_TvsN_cancer
Visualize Single Gene Univariable Cox Result from Toil Data Hubvis_unicox_tree