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.

fetch() fetch_dense_values() fetch_sparse_values() fetch_dataset_samples() fetch_dataset_identifiers() has_probeMap()

Fetch Data from UCSC Xena Hosts

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