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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.