Version 0.2.0: August 5, 2019

Deprecated:

• function analyzeClones is deprecated. The clonal analysis has been added to the main function defineClonesScoper as an argument analyze_clones.
• the out put class is deprecated. Results would be reported as a list if argument analyze_clones set to be true, otherwise a single dataframe is returned.
• plot_neighborhoods from clonal analysis has been deprecated.
• neighborhoods from clonal analysis has been deprecated.

General:

• New models, hierarchical for hierarchical-clustering based, and identical for clustering among identical junction sequences are added.
• New method for spectral-clustering based model has been added through the vj in argument method.

Clonal analysis:

• Switched the meaning of the “inter” and “intra” labels in calculateInterVsIntra function. 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 plotInterVsIntra output 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.