NEWS

---

UCSCXenaTools 1.6.0

• Totally 2486 datasets are included in the current list.
• Single cell hub was found disabled.
• GDC hub was completely updated. The old GDC hub has been renamed to gdcHubV18.

UCSCXenaTools 1.5.0

• Bugs fixed.
• Removed useless action or check config files.
• Removed the XenaShiny() function to reduce the dependencies.
• Updated XenaData. Only minor datasets change found from previous data release.
• Hiplot mirror is down, so we removed its usage in documentation (not delete internal code).
• Added two new queries from xenaPython.

UCSCXenaTools 1.4.8 (2022-06-20)

• Updated to latest Xena dataset list.

UCSCXenaTools 1.4.7 (2021-09-15)

• 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 (2021-07-17)

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

UCSCXenaTools 1.4.5 (2021-05-27)

• 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 (2021-04-06)

• 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 (2021-03-22)

• Implemented using hiplot for fetch() functions.

UCSCXenaTools 1.4.1

• Removed unpublished Xena hub TDI.

UCSCXenaTools 1.4.0 (2021-01-19)

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

UCSCXenaTools 1.3.6 (2020-11-23)

• 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 (2020-11-14)

• Added TDI data Hub containing 9 new datasets.

UCSCXenaTools 1.3.4 (2020-09-30)

• Updated UCSC Xena datasets, now 1670 datasets available.

UCSCXenaTools 1.3.3 (2020-08-05)

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

UCSCXenaTools 1.3.2 (2020-07-14)

• 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 (2020-03-18)

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

UCSCXenaTools 1.3.0 (2020-02-26)

• 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.