Changes in version 0.99.9999999 - Added magick to Suggests in order to fix BioConductor build error on a specific Linux OS. Changes in version 0.99.999999 - Reduced time of some Examples. Changes in version 0.99.99999 - Added GenomeInfoDb to Suggests in DESCRIPTION. Changes in version 0.99.9999 - Re-attempting BioConductor build because of odd dependency error. Changes in version 0.99.999 - Removed LICENSE from .Rbuildignore as this was causing a WARNING during R CMD check. Changes in version 0.99.99 - One final minor change to the DESCRIPTION file r.e. the LICENSE for BioConductor. Changes in version 0.99.9 - Hopefully reduced size of vignette for BioConductor. - Added BioConductor repository to DESCRIPTION file to make installation easier. - Upgraded R version dependency to v4.5.0. - Added dependency on Seurat v5.0 to Suggests in DESCRIPTION & started using layer argument instead of slot when fetching data from a Seurat object. - Removed unnecessary references to the earth package in Roxygen2 documentation that were causing NOTEs in R CMD check. - Added zzz.R that defines all NSE-induced global variables in the package; this resolves a NOTE thrown by R CMD check. Changes in version 0.99.8 - Updated some minor dependencies, etc. for BioConductor submission. Changes in version 0.99.7 - Fixed an incredibly minor Boolean condition warning thrown by BiocCheck. Changes in version 0.99.6 - Changed some function examples & unit tests related to the GLMM coefficient bootstrapping to be faster so as to avoid the "R CMD check exceeds 10mins warning" in BioConductor. Changes in version 0.99.5 - Removed src/Makevars as it was causing compilation issues. - Updated some function examples to have correct syntax. - Fixed some input errors and undefined variables in chooseCandidateGenes(). Changes in version 0.99.4 - Minor error fixes for BioConductor submission. - Updated test suite. - Tweaked some compiler flags. Changes in version 0.99.3 - Minor error fixes for BioConductor submission. Changes in version 0.99.2 - Minor error fixes for BioConductor submission. Changes in version 0.99.1 - Sped up getResultsDE(). - Fixed minor errors for BioConductor submission. Changes in version 0.99.0 - Preparing for BioConductor submission. - Slightly adjusted waldTestGEE() and scoreTestGEE() to be more efficient. Changes in version 0.8.7 - Switched GEE fitting back to use scale.fix = FALSE and substituted a fixed value for the Negative-binomial overdispersion parameter (instead of estimating via method-of-moments) as it improves model fits. - Added option to use a Lagrange Multiplier (Score) test for GEE mode instead of the default Wald test. The relevant argument is gee.test in testDynamic(). - Updated documentation and some tests. - Added column called Null_Fit_Notes to output from getResultsDE() to describe when and how null models fail. This doesn't happen frequently, but it's good info to have when it does. - Expanded test suite to include C++ functions. - Fixed incorrectly-implemented Lagrange Multiplier test after initial code was seen to be incorrect. See this paper for the relevant implementation details. Changes in version 0.8.6 - Changed GEE fitting to use scale.fix = TRUE throughout the package, as it appears to be faster and more statistically efficient based on simulated data benchmarking. Changes in version 0.8.5 - Minor bug fixes. - More improved matrix operations using RcppEigen. - Improved support for cell_data_set objects from monocle3. - Sped up GLMM mode. Changes in version 0.8.4 - Minor bug fixes. - Improved matrix inversion through judicious usage of C++. - Added S3 method summary.scLANE() to be used on output from testDynamic(). Changes in version 0.8.3 - Sped up GLMM mode. - Switched GEE mode to use model-based variance and made computation of sandwich variance-covariance matrix conditional to speed things up and reduce memory usage. Changes in version 0.8.2 - Sped up the NB LASSSO implementation in fitGLMM(). - Fixed some errors related to intercept-only marge models. - Added DF and KC corrections to new function biasCorrectGEE(), usage of which is set to FALSE by default in testDynamic(). - Added support for monocle3 objects of class cell_data_set throughout the package, notably in testDynamic(). Changes in version 0.8.1 - Added small-sample bias correction method to GEE sandwich variance-covariance matrix, results in smaller Wald test statistics. - Parallelized getResultsDE() using future backend. - Added a function called chooseCandidateGenes() to identify good genes for trajectory DE testing based on mean / SD expression and sparsity. Changes in version 0.8.0 - Added implicit regularization of selected basis functions to the GLMM mode using a NB LASSO. - Switched candidate knot subsampling to a uniform sequence of candidate knots across pseudotime's support. Changes in version 0.7.9 - Added geneProgramDrivers() function to compute & test correlations of expression with gene module scores. - Updated documentation & unit tests. - Added geneProgramSignificance() function to estimate associations between gene program module scores and pseudotime. Changes in version 0.7.8 - Added progress bar to testDynamic(). - Changed parallel backend in testDynamic() from doParallel to doSNOW in order to make this possible. - Updated documentation with more runnable examples. - Passing BiocCheck with no errors. - Reduced set of exported functions to just what's necessary for model fitting & downstream analysis. - Reverted changes made to null model scoring internally that lead to worse knot selection i.e., knot selection is improved now. Changes in version 0.7.7 - Added DOI badge to README. - Better compression of included datasets. - Added geneProgramScoring() for module scoring of dynamic gene clusters. - Added plotModelCoefs() to annotate gene dynamics plots with a table of model coefficients. - Added citation file with link to Zenodo repository (until preprint is up). - Added runnable examples to most functions. Changes in version 0.7.6 - Added Zenodo tracking. - Added simulated dataset to data/. Changes in version 0.7.5 - Preparing for BioConductor submission i.e., reformatting code, adding documentation, etc. - Added convolution function npConvolve() to be used for e.g., heatmap smoothing. Changes in version 0.7.4 - Added the getKnotDist() function to pull the set of empirically-identified knots for a user-provided gene set. - Minor enhancements & documentation improvements. Changes in version 0.7.3 - Added a function named embedGenes() that takes a smoothed counts matrix as input & returns PCA & UMAP embeddings along with a graph-based clustering. - Updated the clusterGenes() function to be much more efficient as well as changing the distance metric used to be cosine distance. - Added theme_scLANE() for output plots. - Enhanced documentation. - Increased test coverage. Changes in version 0.7.2 - Added a function named sortGenesHeatmap() that aids in the creation of expression cascade heatmaps by sorting genes according to where in pseudotime their peak expression is. - Changed the parameter approx.knot in the testDynamic() function to use (stochasticity-controlled) subsampling instead of seq() to reduce candidate knot space. - Added summarizeModels() to sum up slopes across pseudotime intervals. Changes in version 0.7.1 - Changed input format of all functions to allow counts matrices formatted as SingleCellExperiment or Seurat objects, sparse matrices, or dense matrices. - Updated visualization functions to reflect changes made in ggplot2 v3.4 (mostly changing the size parameter in line-based geoms to be linewidth instead). Changes in version 0.6.3 - Added a NEWS.md file to track changes to the package.