- Fix partition calculation when clusters are widely separated.
- Fix possible column selection error in plot_cells().
- Work around conflict between SingleCellExperiment and tictoc packages.
- Fix missing DelayedArray conversion in sparse_prcomp_irlba().
- Relax test for rowname consistency in transfer_cell_labels().
- Update URLs in load_worm_*() functions.
- Minor bug fixes.
- Project data set onto a reference data set.
- Annotation label transfer using projection.
- Negative binomial mixed models in fit_models.
- Use annoy nearest neighbor functions.
- Save and load Monocle objects and dimensional reduction models.
- Store matrix identifiers for versioning.
- Documentation improvements.
- Cell_data_set internal rearrangements and additions.
- Set cluster_cells random_seed parameter default to 42.
- Added ability to change aggregation function to aggregate_gene_expression(), and moved scaling to be compatible with multiple aggregation policies
- Fixed some plotting issues.
- Add label_principal_points option to plot_cells to assist with identifying root_pr_nodes in order_cells.
- Documentation and error reports improvements.
- Fix fit_models tests for NA/Inf/NaNs.
- Refine gene loadings calculations in find_gene_modules.
- Test for convergence failure in top_markers,
- Added clear_cds parameter to choose_cells().
- Documentation and error reports improvements.
- Fixed issue #316, top_marker()
- Fixed issue #346, find_gene_modules()
- Added load_mm_data() to load data from matrix market sparse file and gene and cell data files.
- Added rann.k parameter to learn_graph().
- Added speedglm.maxiter parameter to top_marker().
- Fixed combine_cds() issues.
- Fixed learn_graph(use_partition=FALSE) issue
- Fixed batchelor::fastMNN(pc.input) deprecation issue
- Fixed choose_graph_segments() issue.
- Fixed missing gaussian family in fit_models().
- Fixed add pseudocount to violin plot.
- Fixed add detect_genes() to fit_models() if needed.
- Fixed compare_models() issues.
- Fixed check for undefined values in fit_models() formula.
- Fixed plot_cells() plotting order issue.
- Fixed find_gene_modules() run-to-run variation issue.
- Fixed rlist package namespace collision.
- Fixed allow short gene names in aggregate_gene_expression(gene_group_df).
- 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.