Resubmission after babelwhale was removed from CRAN.
DOCUMENTATION: Add vignette for working with AnnData objects.
DOCUMENTATION: Add vignette for working with SingleCellExperiment objects.
DOCUMENTATION: Create pkgdown site.
DOCUMENTATION: Update citEntry to bibentry.
DOCUMENTATION: Reduce execution time of examples by downscaling the example dataset.
draw_trajectory_heatmap()
.Fix ahead of dplyr 1.0 release.
Resubmission of SCORPIUS. SCORPIUS was removed from CRAN because dynwrap was removed from CRAN.
Added a vignette for using SCORPIUS to analyse Seurat data.
ti_scorpius()
wrapper to SCORPIUS.Use RANN::nn2()
instead of own nearest neighbour functions.
Remove deprecated functions.
Use lmds
instead of dyndimred
.
draw_trajectory_plot()
and draw_trajectory_heatmap()
.Fixed internal function check_numeric_matrix()
such that it does not run for ages when applied to
a large sparse matrix.
Minor improvement in infer_initial_trajectory()
when calculating the distance from points to
along candidate segments.
infer_trajectory()
: Use princurve's approx_points
parameter, which greatly speeds up
for trajectory inference for large number of samples.calculate_distance()
instead of correlation_distance()
and euclidean_distance()
.Vignettes were updated.
Added cran-comments.md
.
Added recent news (inst/NEWS.md
).
Added citation information (inst/CITATION
).
Added support for sparsity in extract_modules()
and dimensionality_reduction()
.
Use scaling functions from dynutils (scale_minmax()
, scale_quantile()
, scale_uniform()
).
Expanded unit tests.
Renormalise the original ginhoux data using dynnormaliser and rerun all vignettes.
Moved cmdscale_withlandmarks()
to dyndimred.
extract_modules()
: smooth.spline()
now requires at least 4 unique values.evaluate_trajectory()
and evaluate_dim_red()
.
Use dyneval::evaluate_ti_method()
instead.MINOR CHANGE: Depend on dynutils for distance functions.
MAJOR CHANGE reduce_dimensionality()
: Merge reduce_dimensionality_landmarked
and reduce_dimensionality functions.
REMOVAL: Removed outlier_filter()
; there are much better scRNA-seq preprocessing
pipelines in existance by now.
MINOR CHANGE: Update for princurve 2.0.2.
REMOVAL: Removed deprecated functions infer.trajectory()
, reduce.dimensionality
, and so on.
DOCUMENTATION: Various fixes.
TESTING: Calculate code coverage on travis.
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