NEWS.md

In UCSCXenaTools: Download and Explore Datasets from UCSC Xena Data Hubs

UCSCXenaTools 1.4.8

• Updated to latest Xena dataset list.

UCSCXenaTools 1.4.7

• 3 datasets were added into XenaData.

[1] "TCGA_survival_data_2.txt"                                  
[2] "clinical_CellLinePolyA_21.06_2021-06-15.tsv"               
[3] "CellLinePolyA_21.06_hugo_log2tpm_58581genes_2021-06-15.tsv"

• Added support for gene symbol checking and data cache in fetch().

UCSCXenaTools 1.4.6

• Added code to check hiplot server status.
• Fixed check warnings to follow CRAN policy (#36).

UCSCXenaTools 1.4.5

• Fixed the download bug for pan-cancer data hub due to unvalid URL. url_encode() is added internally to transform reserved characters (/ is kept).
• Fixed the download bug because UCSCXenaShiny mutate the result of XenaQuery() and thus change the column number. This bug will not affect XenaTools itself.

UCSCXenaTools 1.4.4

• Fixed the download bug because UCSCXenaShiny mutate the result of XenaQuery() and thus change the column order. This bug will not affect XenaTools itself.

UCSCXenaTools 1.4.3

• Implemented using hiplot for fetch() functions.

UCSCXenaTools 1.4.1 (1.4.2)

• Removed unpublished Xena hub TDI.

UCSCXenaTools 1.4.0

• Supported downloading data from Hiplot mirror site (https://xena.hiplot.com.cn/).

UCSCXenaTools 1.3.6

• Fixed a bug about try times for data download.
• Make sure a message instead of an error will be returned if download process failed.

UCSCXenaTools 1.3.5

• Added TDI data Hub containing 9 new datasets.

UCSCXenaTools 1.3.4

• Updated UCSC Xena datasets, now 1670 datasets available.

UCSCXenaTools 1.3.3

• Added fetch_sparse_values() function.
• Updated treehouse URL.
• Added treehouse datasets.

UCSCXenaTools 1.3.2

• Fixed bug about an error happened when querying mutation data.
• Dropped "Treehouse" data hub.
• Updated code to update Xena hub datasets.

UCSCXenaTools 1.3.1

• Added max_try option in query and download functions, so they can handle internet connection issue better

UCSCXenaTools 1.3.0

• Added a new data hub: PCAWG Xena Hub (#24).
• Added a new data hub: Kids First Xena Hub (#24).
• Updated data update function more robustly.

UCSCXenaTools documentation built on June 20, 2022, 9:05 a.m.