All notable changes will be documented in this file.
fit_nb_offset
v2
: messages are only invoked if verbosity > 1. fit_nb_offset
to support vst.flavor='v2' by defaultstd::random_shuffle
-> std::shuffle
)latent_var
when vst.flavor="v2"
get_nz_median2
to support genes
argument; thanks @boomanaiden154 and @ScreachingFire. #155get_nz_median
with faster alternative get_nz_median2
across all callsget_nz_median
make_cell_attr
to be flexible for named vectors; thanks @moi-taga #171make.sparse
to handle dgCMatrix
coercsions 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 countsfuture_lapply()
callsdiff_mean_test()
compare
argument to the nonparametric differential expression test diff_mean_test()
to allow for multiple comparisons and various ways to specify which groups to comparevst()
and diff_mean_test()
diff_mean_test()
labels
argument to group_labels
in diff_mean_test()
bw.nrd0
glmGamPoi
(only affected runs with a batch variable set)qpoisson
method for parameter estimation that uses fast Rcpp quasi poisson regression where possible (based on Rfast
package); this adds RcppArmadillo
dependencypoisson_fast
method (replaced by qpoisson
)matrixStats
package and remove RcppEigen
dependencymatch.call()
in vst()
when called via do.call
glmGamPoi
as method to estimate the model parameters; thanks @yuhanH for his pull requesttheta.mm
ortheta.ml
to estimate theta when method = 'poisson'
or method = 'nb_fast'
poisson_fast
method for parameter estimation that uses the speedglm
package and theta.mm
by defaultplot_model_pars
vst
functiondgCMatrix
) - might come in handy some time1 + m / theta
where m is the geometric mean of the observed counts) not log10(theta)
; old behavior available via theta_regularization
parameterverbosity
parameter controls all output: 0 for no output, 1 for only messages, 2 for messages and progress barsAdd the following code to your website.
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