- Adding expanded functionality to
combineBCR()andclonalCluster()- Add new metrics beyond normalized Levenshtein edit distances
- Allow for raw and normalized-based calculations
- Allow for distance matrices to allow for alignment
- Added support for declaring chains = "IGL", "IGK" or "Light" to get all light chains in downstream quantification
- Fixed handling of multiple chains
combineBCR(), specifically in formatting CTstrict
Update to 2.6.0 to match Bioconductor Release 3.22 on 2025/10/30
- Fixed order.by issue in
positionalProperty() - Fixed individual chain call for
combineExpression() - Fixed issue with removing kmer with ";" in
percentKmer()
- Fixed chain handling for BCR genes in
percentGeneUsage()and propagates to wrappers:percentGenes,percentVJandvizGenes
- Fixed passing group.by for
combineBCR()
- Update unit tests for ggplot2 v4
- Fixed clonalProportion calculation to use grouping properly during
combineExpression() - Fixed immunarch support for
exportClones()- TRA/Light chain column handling
- Added support for mouse genes in
quietBCRgenes()andquietTCRgenes()
- Introduced pairwise calculations to
StartracDiversity() - Internal function conversion for
clonalSizeDistribution()- remove cubature, truncdist and VGAM from dependencies. - Increased speed of
clonalSizeDistribution()
- Update/Improve code for
loadContigs() - Consolidated support for discrete AIRR formats under the umbrella of AIRR
- Added
"tcrpheno"andimmunarchtoexportClones() - 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 immApexcalculateFrequency()positionalEntropy()refactored to minimize dependencies and use immApexcalculateEntropy()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 immApexcalculateMotiffor 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 matrixcombineBCR()offers single/dual chain clustering, aa or nt sequences, adaptive filtering of V and J genes and normalized or straight edit distance calculationspercentGeneUsage()now is the underlying function forpercentGenes(),percentVJ(), andvizGenes()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
clonalCompare()issue with plotting a 0 row data frame now errors with messageclonalScatter()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()
- Update internal
.parseContigsto function with more complex groupings - Add
annotateInvariant()functionality for mouse and human TCRs - Add
quietTCRgenes(),quietBCRgenes(),quietVDJgenes() - Fixed issue with
clonalCompare()assertthat statements - Started integration with immApex API package
- Fixed issue with denominator in
getCirclize() - Fixing chain issue with clonalCompare() - expanded assertthat statement
- Rebasing for the purposes of Bioconductor version 3.20
- Added support for BCRs for loading ParseBio sequences.
- Added
quietBCRgenes()andquietTCRgenes()from Ibex and Trex andquietVDJgenes()as a convenience that runs both. The functions filter out known TCR and/or BCR gene signatures.
- Added
Seuratto theSuggestsfield in the DESCRIPTION file.
- Added
getContigDoublets()experimental function to identify TCR and BCR doublets as a preprocessing step tocombineExpression() - Added proportion argument to
clonalCompare()so that when set to FALSE, the comparison will be based on frequency normalized by per-sample repertoire diversity.
- 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
- added type checks using assertthat
- updated conditional statements in constructConDFAndparseTCR.cpp
- Fixed issue in
clonalQuant()and factor-based group.by variable
getCirclize()refactored to prevent assumptions and added include.self argument- Added
.count.clones()internal function forgetCirclize()andclonalNetwork() - 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 issue with
positionalProperty()and removing non-amino acids. - Fixed IGH/K/L mistaking gene issue in
vizGenes() - Add error message for NULL results in
clonalCluster()with export.graph = TRUE - Fixed issue with "full.clones" missing in
combineExpression()when using 1 chain
- 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()andcombineTCR()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
clonalOverlay()arguments now cutpoint and use cut.category to select either clonalProportion or clonalFrequency
- 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(), andclonalAbundance() - x.axis parameter in
clonalDiversity()separated from group.by parameter - filtering chains will not eliminate none matching chains.
- 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
- checkContigs() function to quantify the percentages of NA values by genes or sequences
- exportClones to clonalNetwork() to isolate clones shared across identities.
- 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
- Added
getCirclize()
- 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
- Changed the access of the sample data to github.io repo: readRDS(url("https://ncborcherding.github.io/vignettes/scRepertoire_example.rds"))
- Removed Startrac-based functions in order to pass build on Bioconductor.
DEPRECATED AND DEFUNCT
- Deprecate StartracDiversity()
SIGNIFICANT USER-VISIBLE CHANGES
- Added support for
SingleCellExperimentformat.
DEPRECATED AND DEFUNCT
- Deprecate combineSeurat in favor or combineExpression().
- Deprecate seurat2List in favor of expression2List().