UNDERLYING CHANGES

  • 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()

UNDERLYING CHANGES

  • Modified support for Omniscope format to allow for dual chains
  • Added ParseBio support in to 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

UNDERLYING CHANGES

UNDERLYING CHANGES

  • clonalOverlay() arguments now cutpoint and use cut.category to select either clonalProportion or clonalFrequency

NEW FEATURES

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()
  • Rebasing for the purposes of bioconductor version
  • Fixed combineBCR() to allow for non-related sequences

NEW FEATURES

  • checkContigs() function to quantify the percentages of NA values by genes or sequences
  • exportClones to clonalNetwork() to isolate clones shared across identities.

UNDERLYING CHANGES

  • Fix issue with clonalDiversity() and skipping boots
  • Fixing underlying assumptions with clonalBias()
  • Adding reads variable to parseAIRR
  • Fixing handling of samples parameter in combine contain functions
  • removed need to relevel the cloneType factor after combineExpression()
  • set up lapply() for combineBCR() and clusterTCR() - no more pairwise distance matrix calculation
  • loadContigs() support for data.frames or lists of contigs
  • Added examples for loadContigs() to test function
  • Removed requirement for T cell type designation - will combine A/B and G/D simultaneously
  • Updated combineBCR() to chunk nucleotide edit distance calculations by V gene and give option to skip edit distance calculation with call.related.clones = FALSE
  • Updated clusterTCR() to use lvcompare() function and base edit distances of V gene usage.
  • Fix misspellings for parse contains functions
  • Optimize WAT3R and 10x loadContigs()
  • Remove combineTRUST4 - superseded by loadContigs()
  • Added support of TRUST4 for combineBCR()
  • Added support for BD in loadContigs()
  • loadContigs() TRUST4 parsing allows for all NA values in a chain
  • combineExpression() group.by = NULL will now collapse the whole list.
  • ClonalDiversity() now has skip.boots to stop bootstrapping and downsampling
  • Rebumping the version change with new release of Bioconductor
  • Added mean call to the heatmap of vizGenes()
  • To combineTCR, filteringMulti now checks to remove list elements with 0 cells.
  • Removed top_n() call as it is now deprecated, using slice_max() without ties.
  • Add arrange() call during parseTCR() to organize the chains
  • Correct the gd flip in the combineContig and subsequent functions
  • Removed viridis call in the clonalNetwork() function that was leading to errors
  • Matched syntax for strict clonotype in combineBCR()
  • Added group.by variable to all applicable visualizations
  • Added return.boots to clonalDiversity(), allow for export of all bootstrapped values
  • modified grabMeta() internal function to no longer assume the active Identity is clusters.
  • checkBlanks() now checks if a blank was detected before trying to remove it
  • clonalNetwork() automatically resulted in default error message, bug now removed.
  • clonotypeBias now adds z-score of bias when matrix is exported. exportTable parameter is now fixed.
  • Added loadContigs for non-10X formatted single-cell data
  • removed combineTRUST4, superseded by loadContigs
  • combineTCR() now allows for > 3 recovered TCRs per barcode
  • Readded the filtering steps to combineTCR(), will detect if data is from 10X and automatically remove nonproductive or multi chains.
  • Updated parseTCR() to include evaluation for gamma/delta chains.
  • Arbitrarily numbering system to match new bio conductor dev version
  • highlightClonotypes() now returns the specific clones instead of clonotype 1, …
  • compareClonotypes numbers parameter now for group-wide numbers and not overall top X numbers
  • Fixed issue with clonalDiversity that cause errors when group.by parameter was used.
  • modified parseBCR() to reduce complexity and assume lambda >> kappa
  • fixed clusterTCR() function broken with Seurat Objects
  • checkContigs no ensures data frames and that “” are converted into NAs
  • modified makeGenes() internal function changing na.omit to str_replace_na() and separating the BCR calls by chain to prevent combination errors.
  • Modified parseBCR() to check for contents of the chains. Resolve issue with placing light chain into heavy chain slots when 2 contigs are present.
  • Updated checkBlanks to include NA evaluation and placed the check in all .viz functions
  • Added clonalNetwork() function
  • Modified diversity visualization to remove outliers and place graphs on a single line
  • Modified clonalOverlay() to use new internal getCoord() function like clonalNetwork()
  • Added threshold parameter to clonesizeDistribution()
  • Added support for single-cell objects to clusterTCR()
  • Modification in clusterTCR() and combineBCR() to speed up the comparison and use less memory
  • FilteringMulti, now isolates the top contig by chain, then for barcodes with chains > 2, isolates the top expressing chains. This substantially increases the speed of the filtering step.
  • Modified makeGenes() internal function to use strings str_c()
  • Added threshold parameter to combineTRUST4 for B cell manipulation
  • Changed combineTCR function to prevent cell type mix up and clarified in function documentation.
  • vizGenes can now be used to look at other component genes of the receptor and “separate” parameter was replaced by “y.axis” parameter.
  • Added clonotypeBias() function for inter-cluster comparison.
  • Fixed clusterTCR() and combineBCR() assumption that you will have unrelated clones.
  • CombineBCR() auto naming function updated to actually name the list elements.
  • Added createHTOContigList() function to create contain list of multiplexed experiments. Fixed issue with groupBy variable
  • Added Inv.Pielou matric to diversity call - this is essentially 1-shannon/ln(length). Due to the bootstrapping the length with be constant.
  • Added include.na and split.by to occupiedscRepertoire and changed labeling depending on frequency vs proportion
  • Added support for single-cell objects for most visualizations, list organizing by single-cell object can be called using split.by variable
  • All group and groupBy parameters are now group.by.
  • This is the new numbering scheme apologies - we are all up-to-date now and now cell ranger >= 5 will # work on bioconductor, so let’s all just take that as a win.
  • added dot.size parameter to scatterClonotype
  • filteringMulti now subsets clonotypes with contains >=2, to prevent 2 of the same chains
  • changed how coldata is added to SCE objects using merge instead of union
  • Can now add BCR and TCR simultaneously by making large list
  • scatter plotting code is not so ugly and allows for user to select dot.size as a variable on the x or y axis
  • Removed regressClonotype function - too many dependencies required, adding an additional vignette to go through the process
  • Added chain option to visualizations and combineExpression to allow users to facilitate single chains - removed chain option from combineTCR/BCR/TRUST4 (the combined object will have both chains no matter what)
  • Added NA filter to combineTCR/BCR/TRUST4 for cell barcodes with only NA values
  • Added NA filter to expression2List() for cells with NA clonotypes.
  • Updated VizGene to order the genes automatically by highest to lowest variance
  • Updated VizGene to pull the correct genes based on selection
  • Updated parse method - old version had issue with place V–>J–>D in the TRB/Heavy chains
  • Simplified the clonalDiversity() to allow for more options in organizing plot and box plots.
  • CombineExpression() adds the groupBy variable to Frequency, allowing for multiple calculations to be saved in the meta data.
  • Default color scheme now uses viridis plasma, because it I am on transfusion medicine.
  • added the combineTRUST4 function to parse contigs from TUST4 pipeline
  • added the filter of contigs by chain in the combineTCR, combineBCR, and combineTRUST4 functions
  • no longer require the ID in the combineTCR/BCR/TRUST4 functions
  • added jaccard index for overlap analysis
  • replaced vizVgene with vizGene - allowing users to look at any gene in the combinedContig object
  • Fixed coloring scale on the overlap analysis
  • Added regressClonotype function using harmony to remove the clonotype effect on feature space
  • allowed occupiedRepertoire to use proportion.
  • added scatterClonotype function to Viz.R
  • number of changes to the parseTCR/BCR functions to limit assumptions
  • Changed grabMeta to include assessment of colnames
  • fixed lengthDF handling of single chains with multi chains stored - ;
  • Added labels to alluvialClonotype and occupiedClonotype plotting
  • replaced hammingCompare with lvCompare to enable superior clonotype calling in combineBCR function.
  • added proportion to combineExpression() function so users no longer need to know absolute frequencies when combining the contiguous information.
  • added clusterTCR() and clonalOverlay() functions.
  • added downsampling to the diversity calculations
  • replaced hammingCompare with lvCompare to enable superior clonotype calling in combineBCR function.
  • added proportion to combineExpression() function so users no longer need to know absolute frequencies when combining the contiguous information.
  • added clusterTCR() and clonalOverlay() functions.
  • added downsampling to the diversity calculations
  • Clonal Overlap Coefficient issue fixed, was comparing unique barcodes and not clonotypes
  • Added function checkBlanks to remove list elements without clonotypes, this prevents errors for visualizations
  • Re-added Startrac metrics by stripping down the package and adding it piecemeal
  • Heavily modified dependencies to reduce total number
  • removed dependencies ggfittext and ggdendrogram
  • clonesizeDistribution now returns a plot() function
  • Updated author information in the vignette
  • Updated NEWS formatting
  • Edited DESCRIPTION to Single Cell Experiment R package
  • Updated information in the vignette
  • Modified numerator for index function
  • Removed bracket from indexing function
  • Added exportTable to remaining viz functions
  • Modified morisita index to correct error
  • Reducing the size of the screp_example to fulfill < 5 mB requirement. Randomly samples 100 cells and removed RNA counts from Seurat object
  • Updated compareClonotype to allow for clonotype comparisons
  • Bioconductor did not detect the version update.
  • Bioconductor had no love - changed the Seurat package to imports instead of required, see if that will address the compiling issue that results in a killed: 9 error.
  • Passed checks on system, let’s see how much bioconductor hates it
  • But really this time, changed the colData import
  • Changed colData import
  • Added screp_example data to package
  • Added visVgene function for visualizing the distribution of V genes in TCR
  • Added support for monocle to combineExpression function
  • Updated documentation for combineTCR() and combineBCR()
  • Updated documentation to utilize SingleCellExperiment formats
  • Updated Vignette to utilize SingleCellExperiment formats
  • Added Author information to vignette
  • Add intro and conclusion to vignette
  • Removed html knitted vignette
  • Removed descriptive code snippets
  • Modified expression2List() to allow for variables across meta data
  • Changed R (>= 3.6) to R (>= 4.0)
  • Changed DESCRIPTION version to 0.99.0
  • Removed file seurat_example.rda, accidentally committed
  • Deleted git attributes
  • reduced Seurat object size for alluvialClonotype in vignette
  • Changed the alluvialClonotype assessment to account for only 1 condition
  • Removed Startrac-based functions in order to pass build on Bioconductor.

DEPRECATED AND DEFUNCT

  • Deprecate StartracDiversity()

SIGNIFICANT USER-VISIBLE CHANGES

  • Added support for SingleCellExperiment format.

DEPRECATED AND DEFUNCT

  • Deprecate combineSeurat in favor or combineExpression().
  • Deprecate seurat2List in favor of expression2List().