#VERSION BUMP FOR BIOCONDUCTOR
- 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().