Download and Explore Datasets from UCSC Xena Data Hubs

---

Documentation for package ‘UCSCXenaTools’ version 1.6.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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