News

All notable changes will be documented in this file.

[0.3.1] - 2020-10-08

Added

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

Changed

• 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

Fixed

• Fix inefficiency of using match.call() in vst() when called via do.call

[0.3] - 2020-09-19

Added

• 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

Changed

• 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

Fixed

• Some non-regularized model parameters were not plotted

[0.2.1] - 2019-12-17

Added

• Add function to generate data given the output of a vst run
• Add cpp support for dense integer matrices
• Minimum variance parameter added to vst function

[0.2.0] - 2019-04-12

Added

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

Changed

• lots of things