NEWS

---

scLANE 1.1.2

• Trying to fix Seurat slot vs. layer deprecation error once again.

scLANE 1.1.1

• Fixed a deprecation error in geneProgramScoring().

scLANE 0.99.99999999

• Retrying BioConductor build which failed to to internet connectivity issues.

scLANE 0.99.9999999

• Added magick to Suggests in order to fix BioConductor build error on a specific Linux OS.

scLANE 0.99.999999

• Reduced time of some Examples.

scLANE 0.99.99999

• Added GenomeInfoDb to Suggests in DESCRIPTION.

scLANE 0.99.9999

• Re-attempting BioConductor build because of odd dependency error.

scLANE 0.99.999

• Removed LICENSE from .Rbuildignore as this was causing a WARNING during R CMD check.

scLANE 0.99.99

• One final minor change to the DESCRIPTION file r.e. the LICENSE for BioConductor.

scLANE 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.

scLANE 0.99.8

• Updated some minor dependencies, etc. for BioConductor submission.

scLANE 0.99.7

• Fixed an incredibly minor Boolean condition warning thrown by BiocCheck.

scLANE 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.

scLANE 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().

scLANE 0.99.4

• Minor error fixes for BioConductor submission.
• Updated test suite.
• Tweaked some compiler flags.

scLANE 0.99.3

• Minor error fixes for BioConductor submission.

scLANE 0.99.2

• Minor error fixes for BioConductor submission.

scLANE 0.99.1

• Sped up getResultsDE().
• Fixed minor errors for BioConductor submission.

scLANE 0.99.0

• Preparing for BioConductor submission.
• Slightly adjusted waldTestGEE() and scoreTestGEE() to be more efficient.

scLANE 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.

scLANE 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.

scLANE 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.

scLANE 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().

scLANE 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.

scLANE 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().

scLANE 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.

scLANE 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.

scLANE 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.

scLANE 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.

scLANE 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.

scLANE 0.7.6

• Added Zenodo tracking.
• Added simulated dataset to data/.

scLANE 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.

scLANE 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.

scLANE 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.

scLANE 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.

scLANE 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).

scLANE 0.6.3

• Added a NEWS.md file to track changes to the package.