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 princurveâs 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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