News

All notable changes will be documented in this file.

[0.3.3] - UNRELEASED

vst.flavor argument to vst() to allow for invoking running updated regularization (sctransform v2, proposed in Satija and Choudhary, 2021. See paper for details.
scale_factor to correct() to allow for a custom library size when correcting counts

compare argument to the nonparametric differential expression test diff_mean_test() to allow for multiple comparisons and various ways to specify which groups to compare
Input checking at various places in vst() and diff_mean_test()

Fix bug where factors in cell attributes gave error when checking for NA, NaN, inf

Ability to control the values of latent variables when calculating corrected counts
Offset model as method, including the ability to use a single estimated theta for all genes
Nonparametric differential expression test for sparse non-negative data

Improve poor coefficient initialization in quasi poisson regression
When plotting model, do not show density by default; change bandwidth to bw.nrd0
Updates to C++ code to use sparse matrices as S4 objects
Add check for NA, NaN, Inf values in cell attributes

Remove biocViews from DESCRIPTION - not needed and was causing problems with deploying shiny apps
Fix bug where a coefficient was given the wrong name when using glmGamPoi (only affected runs with a batch variable set)

Add a qpoisson method for parameter estimation that uses fast Rcpp quasi poisson regression where possible (based on Rfast package); this adds RcppArmadillo dependency

Remove poisson_fast method (replaced by qpoisson)
Use matrixStats package and remove RcppEigen dependency
Use quasi poisson regression where possible
Define cell detection event as counts >= 0.01 (instead of > 0) - this only matters to people playing around with fractional counts (see issue #65)
Internal code restructuring and improvements

Add support for glmGamPoi as method to estimate the model parameters; thanks @yuhanH for his pull request
Add option to use theta.mm ortheta.ml to estimate theta when method = 'poisson' or method = 'nb_fast'
Add a poisson_fast method for parameter estimation that uses the speedglm package and theta.mm by default
Add ability to plot overdispersion factor in plot_model_pars
Add and return time stamps at various steps in the vst function
Add functions to calculate grouped arithmetic and geometric mean per row for sparse matrices (dgCMatrix) - might come in handy some time

Default theta regularization is now based on overdispersion factor (1 + m / theta where m is the geometric mean of the observed counts) not log10(theta); old behavior available via theta_regularization parameter
Refactored model fitting code - is now more efficient when using parallel processing
Changed how message and progress bar output is controlled; integer verbosity parameter controls all output: 0 for no output, 1 for only messages, 2 for messages and progress bars
Increased default bin size (genes being processed simultaneously) from 256 to 500
Better input checking for cell attributes; more efficient calculation of missing ones

Rcpp versions of utility functions
Helper functions to get corrected UMI and variance of pearson residuals for large UMI matrices