Changes in version 2.2.1 #VERSION BUMP FOR BIOCONDUCTOR Changes in version 2.0.8 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 Changes in version 2.0.7 UNDERLYING CHANGES - Fixed issue with "group.by" in clonalOverlap() - Fixed issue with "group.by" in clonalCompare() Changes in version 2.0.6 UNDERLYING CHANGES - Fixed issue with custom column headers for clones Changes in 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 Changes in version 2.0.4 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 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 Changes in version 2.0.3 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 Changes in version 2.0.2 UNDERLYING CHANGES - clonalOccupy() rewrite counting and NA handling Changes in version 2.0.1 UNDERLYING CHANGES - clonalOverlay() arguments now cutpoint and use cut.category to select either clonalProportion or clonalFrequency Changes in version 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() Changes in version 1.11.0 - Rebasing for the purposes of bioconductor version Changes in version 1.7.5 - Fixed combineBCR() to allow for non-related sequences Changes in version 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. Changes in version 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. Changes in version 1.7.2 - ClonalDiversity() now has skip.boots to stop bootstrapping and downsampling Changes in version 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 Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 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() Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 1.2.3 - Changed the access of the sample data to github.io repo: readRDS(url("https://ncborcherding.github.io/vignettes/scRepertoire_example.rds")) Changes in version 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() Changes in version 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 Changes in version 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(). Changes in version 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 Changes in version 1.0.0 - removed dependencies ggfittext and ggdendrogram - clonesizeDistribution now returns a plot() function Changes in version 0.99.18 - Updated author information in the vignette Changes in version 0.99.17 - Updated NEWS formatting - Edited DESCRIPTION to Single Cell Experiment R package - Updated information in the vignette Changes in version 0.99.16 - Added getCirclize() Changes in version 0.99.15 - Modified numerator for index function Changes in version 0.99.14 - Removed bracket from indexing function Changes in version 0.99.13 - Added exportTable to remaining viz functions - Modified morisita index to correct error Changes in version 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 Changes in version 0.99.11 - Updated compareClonotype to allow for clonotype comparisons Changes in version 0.99.10 - Bioconductor did not detect the version update. Changes in version 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. Changes in version 0.99.8 - Passed checks on system, let's see how much bioconductor hates it Changes in version 0.99.7 - But really this time, changed the colData import Changes in version 0.99.6 - Changed colData import Changes in version 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 Changes in version 0.99.4 - Modified expression2List() to allow for variables across meta data Changes in version 0.99.1 - Changed R (>= 3.6) to R (>= 4.0) Changes in version 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