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Standard dataset query and download pipeline

Select, query, download and load datasets.

XenaData
Xena Hub Information
XenaScan()
Scan all rows according to user input by a regular expression
XenaGenerate()
Generate and Subset a XenaHub Object from 'XenaData'
XenaFilter()
Filter a XenaHub Object
XenaBrowse()
View Info of Dataset or Cohort at UCSC Xena Website Using Web browser
XenaQuery()
Query URL of Datasets before Downloading
XenaDownload()
Download Datasets from UCSC Xena Hubs
XenaPrepare()
Prepare (Load) Downloaded Datasets to R

Download a subset of dataset

Download a subset of dataset for target analysis.

One-click download function

Download datasets by setting options in one function.

downloadTCGA()
Easily Download TCGA Data by Several Options
getTCGAdata()
Get TCGA Common Data Sets by Project ID and Property
availTCGA()
Get or Check TCGA Available ProjectID, DataType and FileType
showTCGA()
Show TCGA data structure by Project ID or ALL

Utility

Useful functions.

XenaDataUpdate()
Get or Update Newest Data Information of UCSC Xena Data Hubs
XenaShiny()
Xena Shiny App
hosts()
Get hosts of XenaHub object
cohorts()
Get cohorts of XenaHub object
datasets()
Get datasets of XenaHub object
samples()
Get Samples of a XenaHub object according to 'by' and 'how' action arguments
fetch() fetch_dense_values() fetch_sparse_values() fetch_dataset_samples() fetch_dataset_identifiers() has_probeMap()
Fetch Data from UCSC Xena Hosts
XenaQueryProbeMap()
Query ProbeMap URL of Datasets

Helpers

Helper functions.

xena_default_hosts()
UCSC Xena Default Hosts
to_snake()
Convert camel case to snake case

Class

Class and related function.

XenaHub-class
Class XenaHub
XenaHub()
Generate a XenaHub Object