- Added mutual-nearest-neighbor batch correction (MNNCorrect).
- Switched to leiden-based clustering, dropped reticulate/python dependency.
- Added a mechanism to get the citations used during an analysis get_citations().
- Added non-standard color options for plot_cell_3d.
- Added norm_method = 'none' option for importing pre-normalized data.
- Fixed a bug that effected cell size in plot_cells_3d.
- Added a check for illegal characters in generate_garnett_marker_file.
- Fixed a bug in the alpha parameter in plot_cells.
- Fixed multiple minor reported bugs.
- Added bootstrap bars to plot_percent_cells_positive().
- Added a UMI cutoff for load_cellranger_data().
- Added clear_cds_slots() to clear slots from a cds.
- Added cell_stroke parameter to plot_cells.
- Fixed #154, which actually resulted from a problem in how ncenter was calculated for each partition.
- Fixed an issue that prevents plotting cells by pseudotime when root_cells are passed to order_cells().
- Fixed #167 - NAs from plot_genes_by_group.
- Added a
NEWS.mdfile to track changes to the package. - Added a combine_cds function that will combine cell_data_sets .
- Added a message when duplicate markers are present in generate_garnett_marker_file and option to exclude them.
- Fixed a bug that made expression matrix the wrong class with load_cellranger.