NEWS.md

In cellGeometry: Geometric Single Cell Deconvolution

News

14/04/2026

• Add S3 method for confint() with deconv objects to allow calculation of confidence intervals.
• Add max_similarity() for calculating maximum similarity between cell types.
• Add CV of lambda in deconvolute() [experimental].
• Use $opt element to store call arguments in deconvolute().
• Refine vignette.

19/03/2026

• Improved plot_comp() and plot_path() with option to show cell percentages.

cellGeometry 0.6.2

26/02/2026

• Improved error checks in deconvolute() to help with issue #20.

New features

• Add measurement of bias and variance to tune_deconv().
• Add plot_tunevar() to compare MSE, bias^2 and variance.
• Add S3 method for kappa() to compute the condition number of the spillover matrix.
• Add plot_path() to show how the coefficient paths vary with compensation for either a single bulk sample or a cell subclass.
• Add plot_pred() as an alternative to plot_set() for viewing predicted vs observed results from simulations in a single correlation plot.
• Add zero_fraction argument to generate_samples().

cellGeometry 0.6.1

13/01/2026

• Fix subtle division by near 0 issue in nest_output

New features

• Massive speed up of deconvolute().
• Add ridge parameter lambda to deconvolute() [experimental].
• Add resvar metric to tune_deconv() to examine residual variance of bulk gene expression.

Important change

• deconvolute() no longer returns se and hat in the subclass list element. Standard errors can be obtained with the new function se().
• cores argument has been removed from deconvolute()

Important bugfix

• R 4.5.2 for macOS arm64 (Apple M Macs) has switched to using a faster BLAS (vecLib?) by default, which causes errors with parallelisation in mclapply(). The problem is isolated to R 4.5.2 arm64 for macOS on M Macs; or any version of R for macOS including intel, if vecLib BLAS is being used via a symlink. The solution is to use cores = 1 with deconvolute() and tune_deconv() whenever vecLib BLAS is in use.
• Removed use of pbmcapply::pbmclapply() as this caused problems with R 4.5.2 for macOS arm64 (Apple M* Macs) even with cores=1. This fixes indefinite hanging in tune_deconv() associated with vecLib BLAS.

cellGeometry 0.5.7

11/12/2025

• Change log argument in deconvolute() to logged_bulk. NB. this is a change of logic.

cellGeometry 0.5.6

07/10/2025

• Add residuals.deconv() to allow recalculation of full residuals matrix.

cellGeometry 0.5.5

10/09/2025

• Fix bug in mergeMarkers() if cellMarkers object has no cell grouping vector.

cellGeometry 0.5.4

09/09/2025

• Fix CRAN checks
• Switch from using cat() to message()

cellGeometry 0.5.3

26/08/2025

• Massive speed up (4-5x) in compensation optimisation

cellGeometry 0.5.2

30/07/2025

• Expanded to 3 methods for identifying outlier genes (var.e, Cook's distance, Studentized residuals)
• Improved (nested) parallelisation of tune_deconv()
• Rewrite weights code (faster)

cellGeometry 0.5.0

14/07/2025

• Calculation of SE
• Detection and multipass removal of problematic genes with extreme residuals

cellGeometry 0.2.0

24/01/2025

• This is the initial build of cellGeometry

cellGeometry documentation built on April 20, 2026, 1:06 a.m.