Skip to content

Latest commit

 

History

History
29 lines (24 loc) · 2.04 KB

NEWS.md

File metadata and controls

29 lines (24 loc) · 2.04 KB

Changes in v0.0.3

  • Updated support for v4 vs. v5 Seurat objects.
  • Exposed choice of variational inference algorithm to the user via argument VI.algorithm in findvariableFeaturesBayes().
  • Updated documentation thoroughly.
  • Removed QR decomposition on fixed effects as it wasn't necessary.

Changes in v0.0.2

  • Added conditional support for legacy Seurat v4 objects in addition to the default Seurat v5 objects.
  • Added per-gene estimated posterior variances and dispersions based on NB variance definition, along with credible intervals for each per-gene.
  • Implemented ability to select HVGs by either estimated dispersion or estimated variance in classifyHVGs().
  • Changed model fitting process to support within-chain parallelism as long as enough cores are available.
  • Added function computeNaiveGeneStatistics() to estimate (in a Frequentist manner) per-gene mean, variance, and dispersion.
  • Sped up findvariableFeaturesBayes() via:
    • Adding GPU acculeration support for OpenCL-compatible devices.
    • Performing QR decomposition on covariates before fitting.
    • Added compiler optimization flags for Stan to C++ code conversion.
    • Set normalize = FALSE in call to brms::brm(), which increases efficiency of sampling from approximate posterior.

Changes in v0.0.1

  • Initial package skeleton.
  • Added main function findVariableFeaturesBayes() (still in development right now).
  • Added helper function sampleMarginal() to make sampling from posterior marginal distribution possible.
  • Added support for adding gene statistics metadata to SingleCellExperiment or Seurat objects after estimation.
  • Changed main model backend to brms via cmdstanr instead of INLA, since INLA doesn't appear to support per-group estimation of the Negative-binomial overdispersion parameter.
  • Added function classifyHVGs() to add a label to HVGs in Seurat or SingleCellExperiment object metadata based on several different methods.
  • Added function theme_bayesHVG(), which implements a publication-ready theme for ggplot2.