loadContigs()
and testthatloadContigs()
for BD, Omniscope, and Immcantation formatsloadContigs()
combineBCR()
and combineTCR()
no allow for unproductive contig inclusions with new filterNonproductive parameter.combineBCR()
will now prompt user if samples is not included instead of erroring..lvCompare()
.lvCompare()
only looks at first set of sequences in multi-sequence chain.clonaCluster()
clonalOccupy()
rewrite counting and NA handlingclonalOverlay()
arguments now cutpoint and use cut.category to select either clonalProportion or clonalFrequencypercentAA()
percentGenes()
percentVJ()
percentKmer()
exportClones()
positionalEntropy()
positionalProperty()
clonalCompare()
clonalSizeDistribution()
clonalScatter()
clonalQuant()
highlightClones()
clonalLength()
clonalOccupy()
clonalAbundance()
alluvialClones()
clonalCompare()
to allow for highlighting sequences, relabeling clonotypes.StartracDiversity()
metric re-implemented to remove startrac-class object intermediaryloadContigs()
clonalQuant()
for instance of scale = FALSE and group.by being set.clonalDiversity()
no longer automatically orders samples.clonalQuant()
, clonalLength()
, and clonalAbundance()
clonalDiversity()
separated from group.by parametergetCirclize()
DEPRECATED AND DEFUNCT
SIGNIFICANT USER-VISIBLE CHANGES
SingleCellExperiment
format.DEPRECATED AND DEFUNCT
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