R: Download and Explore Datasets from UCSC Xena Data Hubs

# Download and Explore Datasets from UCSC Xena Data Hubs

## Documentation for package ‘UCSCXenaTools’ version 1.7.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A C D F G H S T U X misc

## -- A --

availTCGA | Get or Check TCGA Available ProjectID, DataType and FileType

## -- C --

cohorts | Get cohorts of XenaHub object

## -- D --

datasets | Get datasets of XenaHub object
downloadTCGA | Easily Download TCGA Data by Several Options

## -- F --

fetch | Fetch Data from UCSC Xena Hosts
fetch_dataset_identifiers | Fetch Data from UCSC Xena Hosts
fetch_dataset_samples | Fetch Data from UCSC Xena Hosts
fetch_dense_values | Fetch Data from UCSC Xena Hosts
fetch_sparse_values | Fetch Data from UCSC Xena Hosts

## -- G --

getTCGAdata | Get TCGA Common Data Sets by Project ID and Property

## -- H --

has_probeMap | Fetch Data from UCSC Xena Hosts
hosts | Get hosts of XenaHub object

## -- S --

samples | Get Samples of a XenaHub object according to 'by' and 'how' action arguments
showTCGA | Show TCGA data structure by Project ID or ALL

## -- T --

to_snake | Convert camel case to snake case

## -- U --

UCSCXenaTools-dynamic | UCSC Xena Dynamic Objects

## -- X --

XenaBrowse | View Info of Dataset or Cohort at UCSC Xena Website Using Web browser
XenaData | Xena Hub Information
XenaDataUpdate | Get or Update Newest Data Information of UCSC Xena Data Hubs
XenaDownload | Download Datasets from UCSC Xena Hubs
XenaFilter | Filter a XenaHub Object
XenaGenerate | Generate and Subset a XenaHub Object from 'XenaData'
XenaHub | Generate a XenaHub Object
XenaHub-class | Class XenaHub
XenaPrepare | Prepare (Load) Downloaded Datasets to R
XenaQuery | Query URL of Datasets before Downloading
XenaQueryProbeMap | Query ProbeMap URL of Datasets
XenaScan | Scan all rows according to user input by a regular expression
xena_default_hosts | UCSC Xena Default Hosts

## -- misc --

.p_all_cohorts | UCSC Xena Dynamic Objects
.p_all_datasets | UCSC Xena Dynamic Objects
.p_all_datasets_n | UCSC Xena Dynamic Objects
.p_all_field_metadata | UCSC Xena Dynamic Objects
.p_cohort_samples | UCSC Xena Dynamic Objects
.p_cohort_summary | UCSC Xena Dynamic Objects
.p_datasets_null_rows | UCSC Xena Dynamic Objects
.p_dataset_fetch | UCSC Xena Dynamic Objects
.p_dataset_field | UCSC Xena Dynamic Objects
.p_dataset_field_examples | UCSC Xena Dynamic Objects
.p_dataset_field_n | UCSC Xena Dynamic Objects
.p_dataset_gene_probes_values | UCSC Xena Dynamic Objects
.p_dataset_gene_probe_avg | UCSC Xena Dynamic Objects
.p_dataset_list | UCSC Xena Dynamic Objects
.p_dataset_metadata | UCSC Xena Dynamic Objects
.p_dataset_probe_signature | UCSC Xena Dynamic Objects
.p_dataset_probe_values | UCSC Xena Dynamic Objects
.p_dataset_samples | UCSC Xena Dynamic Objects
.p_dataset_samples_ndense_matrix | UCSC Xena Dynamic Objects
.p_dataset_sources | UCSC Xena Dynamic Objects
.p_dataset_status | UCSC Xena Dynamic Objects
.p_feature_list | UCSC Xena Dynamic Objects
.p_field_codes | UCSC Xena Dynamic Objects
.p_field_metadata | UCSC Xena Dynamic Objects
.p_gene_transcripts | UCSC Xena Dynamic Objects
.p_match_fields | UCSC Xena Dynamic Objects
.p_probemap_list | UCSC Xena Dynamic Objects
.p_probe_count | UCSC Xena Dynamic Objects
.p_ref_gene_exons | UCSC Xena Dynamic Objects
.p_ref_gene_position | UCSC Xena Dynamic Objects
.p_ref_gene_range | UCSC Xena Dynamic Objects
.p_segmented_data_range | UCSC Xena Dynamic Objects
.p_segment_data_examples | UCSC Xena Dynamic Objects
.p_sparse_data | UCSC Xena Dynamic Objects
.p_sparse_data_examples | UCSC Xena Dynamic Objects
.p_sparse_data_match_field | UCSC Xena Dynamic Objects
.p_sparse_data_match_field_slow | UCSC Xena Dynamic Objects
.p_sparse_data_match_partial_field | UCSC Xena Dynamic Objects
.p_sparse_data_range | UCSC Xena Dynamic Objects
.p_transcript_expression | UCSC Xena Dynamic Objects
.XenaHub | Class XenaHub
.xq_all_cohorts | UCSC Xena Dynamic Objects
.xq_all_datasets | UCSC Xena Dynamic Objects
.xq_all_datasets_n | UCSC Xena Dynamic Objects
.xq_all_field_metadata | UCSC Xena Dynamic Objects
.xq_cohort_samples | UCSC Xena Dynamic Objects
.xq_cohort_summary | UCSC Xena Dynamic Objects
.xq_datasets_null_rows | UCSC Xena Dynamic Objects
.xq_dataset_fetch | UCSC Xena Dynamic Objects
.xq_dataset_field | UCSC Xena Dynamic Objects
.xq_dataset_field_examples | UCSC Xena Dynamic Objects
.xq_dataset_field_n | UCSC Xena Dynamic Objects
.xq_dataset_gene_probes_values | UCSC Xena Dynamic Objects
.xq_dataset_gene_probe_avg | UCSC Xena Dynamic Objects
.xq_dataset_list | UCSC Xena Dynamic Objects
.xq_dataset_metadata | UCSC Xena Dynamic Objects
.xq_dataset_probe_signature | UCSC Xena Dynamic Objects
.xq_dataset_probe_values | UCSC Xena Dynamic Objects
.xq_dataset_samples | UCSC Xena Dynamic Objects
.xq_dataset_samples_ndense_matrix | UCSC Xena Dynamic Objects
.xq_dataset_sources | UCSC Xena Dynamic Objects
.xq_dataset_status | UCSC Xena Dynamic Objects
.xq_feature_list | UCSC Xena Dynamic Objects
.xq_field_codes | UCSC Xena Dynamic Objects
.xq_field_metadata | UCSC Xena Dynamic Objects
.xq_gene_transcripts | UCSC Xena Dynamic Objects
.xq_match_fields | UCSC Xena Dynamic Objects
.xq_probemap_list | UCSC Xena Dynamic Objects
.xq_probe_count | UCSC Xena Dynamic Objects
.xq_ref_gene_exons | UCSC Xena Dynamic Objects
.xq_ref_gene_position | UCSC Xena Dynamic Objects
.xq_ref_gene_range | UCSC Xena Dynamic Objects
.xq_segmented_data_range | UCSC Xena Dynamic Objects
.xq_segment_data_examples | UCSC Xena Dynamic Objects
.xq_sparse_data | UCSC Xena Dynamic Objects
.xq_sparse_data_examples | UCSC Xena Dynamic Objects
.xq_sparse_data_match_field | UCSC Xena Dynamic Objects
.xq_sparse_data_match_field_slow | UCSC Xena Dynamic Objects
.xq_sparse_data_match_partial_field | UCSC Xena Dynamic Objects
.xq_sparse_data_range | UCSC Xena Dynamic Objects
.xq_transcript_expression | UCSC Xena Dynamic Objects