v2.5.0

UNDERLYING CHANGES

• Update/Improve code for loadContigs()
• Consolidated support for discrete AIRR formats under the umbrella of AIRR
• Added "tcrpheno" and immunarch to exportClones()
• Converted exportClones() to base R to reduce dependencies
• Added dandelionR vignette to pkgdown site
• Added tcrpheno vignette to pkgdown site
• percentAA() refactored to minimize dependencies and use immApex
  calculateFrequency()
• positionalEntropy() refactored to minimize dependencies and use immApex
  calculateEntropy()
• clonalDiversity() refactored for performance - it now calculates a
  single diversity metric at a time and includes new estimators like "gini",
  "d50", and supports hill numbers).
• percentKmer() refactored to use immApex calculateMotif for both aa and
  nt sequences. No longer calculates all possible motifs, but only motifs present.
• clonalCluster() now allows for dual-chain clustering, V/J filtering,
  normalized or straight edit distance calculations, and return of clusters,
  igraph objects or adjacency matrix
• combineBCR() offers single/dual chain clustering, aa or nt sequences, adaptive filtering of V and J genes and normalized or straight edit distance calculations
• percentGeneUsage() now is the underlying function for percentGenes(), percentVJ(),
  and vizGenes() and allows for percent, proportion and raw count quantification.
• Added common theme (internal .themeRepertoire()) to all plots and allow users to pass arguments to it

BUG FIXES

• clonalCompare() issue with plotting a 0 row data frame now errors with message
• clonalScatter() group.by/axes call now works for non-single-cell objects
• Fixed issue with NULL and "none" group.by in combineExpression()
• Allowing multi groupings via x.axis and group.by in clonalDiversity()