Version 1.1.0: August 10, 2020¶
- Fixed a bug in the clonal clustering methods causing TCR data to fail.
- Added support for single-cell data in the clonal clustering methods, which
are enabled by defining the optional
Version 1.0.1: May 24, 2020¶
- Fixed a fatal error in
Version 1.0.0: May 15, 2020¶
Backwards Incompatible Changes:
- Changed default expected data format from the Change-O data format to the
AIRR Rearrangement standard. For example: where functions used the column
V_CALL(Change-O) as the default to identify the field that stored the V gene calls, they now use
v_call(AIRR). That means, scripts that relied on default values (previously,
v_call="V_CALL"), will now fail if calls to the functions are not updated to reflect the correct value for the data. If data are in the Change-O format, the current default value
v_call="v_call"will fail to identify the column with the V gene calls as the column
v_calldoesn’t exist. In this case,
v_call="V_CALL"needs to be specified in the function call.
ExampleDbconverted to the AIRR Rearrangement standard and examples updated accordingly.
defineClonesScoperfunction to three functions:
- License changed to AGPL-3.
- Fixed a platform precision incompatibility bug which caused spectral cloning results to be non-reproducible across platforms.
- Added largest distance-to-nearest filter to clustering process.
Version 0.2.0: August 5, 2019¶
analyzeClonesis deprecated. The clonal analysis has been added to the main function
defineClonesScoperas an argument
- the out put class is deprecated. Results would be reported as a list if
analyze_clonesset to be true, otherwise a single dataframe is returned.
plot_neighborhoodsfrom clonal analysis has been deprecated.
neighborhoodsfrom clonal analysis has been deprecated.
- New models,
hierarchicalfor hierarchical-clustering based, and
identicalfor clustering among identical junction sequences are added.
- New method for spectral-clustering based model has been added through the
- Switched the meaning of the “inter” and “intra” labels in
calculateInterVsIntrafunction. Now, “inter” is the label used to form distances that mean between clones, and “intra” is the label used to form distances that mean on the inside, within each clone.
- Changed the
plotInterVsIntraoutput from a density plot to a histogram.
- Changed the way to calculate the effective threshold. Now, desntiy approach is used.
Version 0.1.0: October 4, 2018¶
Initial public release.