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NEWS.md

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Changes in v0.99.0

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

Changes in v0.8.7

  • 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 v0.8.6

  • 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 v0.8.5

  • Minor bug fixes.
  • More improved matrix operations using RcppEigen.
  • Improved support for cell_data_set objects from monocle3.
  • Sped up GLMM mode.

Changes in v0.8.4

  • 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

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.