CHANGES IN VERSION 1.7.2 ------------------------ * 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1.5.3 ------------------------ * Added loadContigs for non-10X formatted single-cell data * removed combineTRUST4, superseded by loadContigs * combineTCR() now allows for 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 1.2.2 ------------------------ # Working on renumbering versions for consistency - this is the new current dev branch # The below have not been implemented into the master branch or the bioconductor version * 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 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 1.1.4 ------------------------ * 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 SingleCellExperiment 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 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 ------------------------ * Removed Startrac-based functions in order to pass build on Bioconductor. DEPRECATED AND DEFUNCT * Deprecate StartracDiversity() CHANGES IN VERSION 1.2.0 ------------------------ The first version of scRepertoire submitted to Bioconductor. SIGNIFICANT USER-VISIBLE CHANGES * Added support for SingleCellExperiement format. DEPRECATED AND DEFUNCT * Deprecate combineSeurat in favor or combineExpression(). * Deprecate seurat2List in favor of expression2List().