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SCORPIUS 1.0.9

• 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.

SCORPIUS 1.0.8

• MINOR CHANGE: Allow adding row annotations to draw_trajectory_heatmap().

SCORPIUS 1.0.7 (2020-05-11)

Fix ahead of dplyr 1.0 release.

• MINOR CHANGE: substitute as.tbl_cube for reshape2::melt.

SCORPIUS 1.0.6 (2020-03-16)

Minor change

• Resubmission of SCORPIUS. SCORPIUS was removed from CRAN because dynwrap was removed from CRAN.

• Added a vignette for using SCORPIUS to analyse Seurat data.

SCORPIUS 1.0.5 (08-12-2019)

Major change

• Added a ti_scorpius() wrapper to SCORPIUS.

Minor change

• Use RANN::nn2() instead of own nearest neighbour functions.

• Remove deprecated functions.

• Use lmds instead of dyndimred.

SCORPIUS 1.0.4 (07-08-2019)

Minor changes

• Added extra customisation parameters to draw_trajectory_plot() and draw_trajectory_heatmap().

Optimisation

• 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.

SCORPIUS 1.0.3 (27-05-2019)

Optimisation

• infer_trajectory(): Use princurve’s approx_points parameter, which greatly speeds up for trajectory inference for large number of samples.

Major changes

• Use dynutils’ calculate_distance() instead of correlation_distance() and euclidean_distance().

Documentation

• 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().

Minor changes

• 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.

Bug fixes

• extract_modules(): smooth.spline() now requires at least 4 unique values.

Deprecation

• Deprecated unused functions evaluate_trajectory() and evaluate_dim_red(). Use dyneval::evaluate_ti_method() instead.

SCORPIUS 1.0.2 (2018-06-29)

• 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.

SCORPIUS 1.0.1 (2018-06-21)

• 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.

SCORPIUS 1.0.0 (2017-09-15)

• Initial release on CRAN.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.