v2.2.1

scRepertoire VERSION 2.2.1

NEW FEATURES

• Added getContigDoublets() experimental function to identify TCR and BCR doublets as a preprocessing step to combineExpression()
• Added proportion argument to clonalCompare() so that when set to FALSE, the comparison will be based on frequency normalized by per-sample repertoire diversity.

UNDERLYING CHANGES

• Fixed issue with single chain output for clonalLength()
• Removed unnecessary code remnant in clonalLength()
• Allow one sample to be plotted by percentVJ()
• Fixed issue with positionalProperty() and exportTable
• Fixed issue with loadContigs() edge case when TRUST4 data only has 1 row.
• convert documentation to use markdown (roxygen2md)
• import lifecycle, purrr, withr
• suppressed "using discrete variable for alpha is not recommended" warning in alluvialClones unit tests.
• Fixed issue with clonalCluster() and exportGraph = TRUE
• improve performance of combineBCR() by a constant factor with C++
• Restructured functions to exportTable before plotting
• Fixed issue with "group.by" in clonalOverlap()
• Fixed issue with "group.by" in clonalCompare()
• Fixed issue with custom column headers for clones

v2.0.5

scRepertoire VERSION 2.0.5

UNDERLYING CHANGES

• added type checks using assertthat
• updated conditional statements in constructConDFAndparseTCR.cpp
• Fixed issue in clonalQuant() and factor-based group.by variable
• Add error message for NULL results in clonalCluster() with export.graph = TRUE
• Fixed issue with "full.clones" missing in combineExpression() when using 1 chain

v2.0.4

scRepertoire VERSION 2.0.4

UNDERLYING CHANGE

• getCirclize() refactored to prevent assumptions and added include.self argument
• Added .count.clones() internal function for getCirclize() and clonalNetwork()
• Added order.by parameter to visualizations to specifically call order of plotting using a vector or can use "alphanumeric" to plot things in order
• Fix issue with clonalLength() and NA handling
• clonalCompare() now retains the original clonal info if using relabel.clones
• Add Dandelion support in to loadContigs() and testthat
• Fixed issue with positionalProperty() assumption that the clones will all have 20 amino acids.
• Fixed IGH/K/L mistaking gene issue in vizGenes()

v2.0.3

scRepertoire VERSION 2.0.3

UNDERLYING CHANGES

• Modified support for Omniscope format to allow for dual chains
• Added ParseBio support int loadContigs() and testthat
• Added support for productive variable to loadContigs() for BD, Omniscope, and Immcantation formats
• Replace numerical indexing with name indexing for loadContigs()
• 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.
• Added base threshold by length for internal .lvCompare()
• Ensured internal .lvcompare() only looks at first set of sequences in multi-sequence chain.
• Fixed bug in exporting graph for clonaCluster()
• Fixed conflict in functions between igraph and dplyr packages
• clonalOccupy() rewrite counting and NA handling (v2.0.2)
• clonalOverlay() arguments now cutpoint and use cut.category to select either clonalProportion or clonalFrequency v(2.0.1)

v2.0.0

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.

UNDERLYING CHANGES

• 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.

DEPRECATED AND DEFUNCT

• Deprecate stripBarcodes()
• Deprecate expression2List() (now only an internal function).
• Deprecate checkContigs()