CHANGES IN VERSION 1.2.1 ------------------------ # Universalizing the versions across GitHub and bioconductor, we are now at 1.2 for bioconductor # and v1.2.1 for the master. Dev branch will be updated to reflect this change to v1.2.2. Apologies #for the confusion. * Updated coding practices based on devtools and bioccheck * Deprecated VizVgene() support - erroring during build and new version in dev branch to visualize any gene * fixed lengthDF handling of single chains with multi chains stored - ; * Changed grabMeta to include assessment of colnames * number of changes to the parseTCR/BCR functions to limit assumptions 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().