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UCSCXenaTools 1.6.1

• Added new single cell hub url.
• Added docs for dynamics.

UCSCXenaTools 1.6.0

• Totally 2511 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

• 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• Removed unpublished Xena hub TDI.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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.