NEWS

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scRepertoire 2.0.0 (2024-01-10)

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()

scRepertoire 1.11.0

• Rebasing for the purposes of bioconductor version

scRepertoire 1.7.5

• Fixed combineBCR() to allow for non-related sequences

scRepertoire 1.7.4

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.

scRepertoire 1.7.3

• 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.

scRepertoire 1.7.2

• ClonalDiversity() now has skip.boots to stop bootstrapping and downsampling

scRepertoire 1.7.0

• 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

scRepertoire 1.5.4

• 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.

scRepertoire 1.5.3

• 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.

scRepertoire 1.5.2

• 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.

scRepertoire 1.3.5

• 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()

scRepertoire 1.3.4

• 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.

scRepertoire 1.3.3

• 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.

scRepertoire 1.3.2

• 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.

scRepertoire 1.2.3

• Changed the access of the sample data to github.io repo: readRDS(url("https://ncborcherding.github.io/vignettes/scRepertoire_example.rds"))

scRepertoire 1.2.2

• 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

• Removed Startrac-based functions in order to pass build on Bioconductor.

DEPRECATED AND DEFUNCT

• Deprecate StartracDiversity()

scRepertoire 1.2.1

• 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

scRepertoire 1.2.0

SIGNIFICANT USER-VISIBLE CHANGES

• Added support for SingleCellExperiment format.

DEPRECATED AND DEFUNCT

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

scRepertoire 1.1.4

• 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

scRepertoire 1.0.0

• removed dependencies ggfittext and ggdendrogram
• clonesizeDistribution now returns a plot() function

scRepertoire 0.99.18

• Updated author information in the vignette

scRepertoire 0.99.17

• Updated NEWS formatting
• Edited DESCRIPTION to Single Cell Experiment R package
• Updated information in the vignette

scRepertoire 0.99.16

• Added getCirclize()

scRepertoire 0.99.15

• Modified numerator for index function

scRepertoire 0.99.14

• Removed bracket from indexing function

scRepertoire 0.99.13

• Added exportTable to remaining viz functions
• Modified morisita index to correct error

scRepertoire 0.99.12

• Reducing the size of the screp_example to fulfill < 5 mB requirement. Randomly samples 100 cells and removed RNA counts from Seurat object

scRepertoire 0.99.11

• Updated compareClonotype to allow for clonotype comparisons

scRepertoire 0.99.10

• Bioconductor did not detect the version update.

scRepertoire 0.99.9

• 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.

scRepertoire 0.99.8

• Passed checks on system, let's see how much bioconductor hates it

scRepertoire 0.99.7

• But really this time, changed the colData import

scRepertoire 0.99.6

• Changed colData import

scRepertoire 0.99.5

• 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

scRepertoire 0.99.4

• Modified expression2List() to allow for variables across meta data

scRepertoire 0.99.1

• Changed R (>= 3.6) to R (>= 4.0)

scRepertoire 0.99.0

• 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