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