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News
All notable changes will be documented in this file.
[0.4.1] - 2023-10-18
Fixed
- Fixed column name setting in
fit_nb_offset
Changed
- Verbose messages when invoking
v2
: messages are only
invoked if verbosity > 1.
[0.4.0] - 2023-09-18
Added
- Add
fit_nb_offset
to support vst.flavor=‘v2’ by
default
Fixed
- Updated cpp utilities to adhere to C++17 standards
(
std::random_shuffle
-> std::shuffle
)
- Handling of extra variables in
latent_var
when
vst.flavor="v2"
Changed
- Changed
get_nz_median2
to support genes
argument; thanks @boomanaiden154 and @ScreachingFire. #155
- Replaced
get_nz_median
with faster alternative
get_nz_median2
across all calls
- Removed
get_nz_median
- Updated
make_cell_attr
to be flexible for named
vectors; thanks @moi-taga #171
[0.3.5] - 2022-09-21
Fixed
- Specify required Matrix version to >= 1.5.0
[0.3.4] - 2022-08-19
Added
- Add
make.sparse
to handle dgCMatrix
coercsions
Fixed
- Convert bitwise operators to boolean operators in utils.cpp
[0.3.3] - 2022-01-13
Added
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
[0.3.2] - 2021-07-28
Added
- Add future.seed = TRUE to all
future_lapply()
calls
Changed
- Wrap MASS::theta.ml() in suppressWarnings()
Fixed
- Fix logical comparison of vectors of length one in
diff_mean_test()
[0.3.2] - 2020-02-11
Added
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()
Changed
- Major speed improvements for
diff_mean_test()
- Changed the
labels
argument to
group_labels
in diff_mean_test()
Fixed
- Fix bug where factors in cell attributes gave error when checking
for NA, NaN, inf
[0.3.2] - 2020-12-16
Added
- 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
Changed
- 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
Fixed
- 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)
[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
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