Release v2.0.0 · BorchLab/scRepertoire

NEW FEATURES

Added percentAA()
Added percentGenes()
Added percentVJ()
Added percentKmer()
Added exportClones()
Added positionalEntropy()
Added positionalProperty()
Changed compareClonotypes to clonalCompare()
Changed clonotypeSizeDistribution to clonalSizeDistribution()
Changed scatterClonotypes to clonalScatter()
Changed quantContig to clonalQuant()
Changed highlightClonotypes to highlightClones()
Changed lengthContigs to clonalLength()
Changed occupiedscRepertoire to clonalOccupy()
Changed abundanceContig to clonalAbundance()
Changed alluvialClonotypes to alluvialClones()
Added features to clonalCompare() to allow for highlighting sequences, relabeling clonotypes.

Removed internal .quiet() function.
.theCall() now allows for a custom header/variable and checks the colnames.
Replaced data arguments to be more descriptive: df is now input.data, dir is now input, and sc is now sc.data
Deep clean on the documentation for each function for increased consistency and explainability
StartracDiversity() metric re-implemented to remove startrac-class object intermediary
Implemented powerTCR locally to reduce dependencies and continue support
Universalized underlying function language and intermediate variables
License change to MIT
group.by and split.by have been consolidated into single group.by parameter
Added support for Immcantation pipeline, .json, Omniscope, and MiXCR formats for loadContigs()
Made GitHub.io website for support/vignettes/FAQ
Restructured NEWS Tracking
Added testthat for all exported and internal functions
Fixed issue with clonalQuant() for instance of scale = FALSE and group.by being set.
clonalDiversity() no longer automatically orders samples.
Remove order parameter from clonalQuant(), clonalLength(), and clonalAbundance()
x.axis parameter in clonalDiversity() separated from group.by parameter
filtering chains will not eliminate none matching chains.