NEWS

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monocle3 1.3.7

Changes

• Fix partition calculation when clusters are widely separated.
• Fix possible column selection error in plot_cells().

monocle3 1.3.0

Changes

• 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.

monocle3 1.2.9

Changes

• 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

Bug fixes

• Fixed some plotting issues.

monocle3 1.0.0

Changes

• Add label_principal_points option to plot_cells to assist with identifying root_pr_nodes in order_cells.

Bug fixes

• 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,

monocle3 0.2.3

Changes

• Added clear_cds parameter to choose_cells().

Bug fixes

• Documentation and error reports improvements.
• Fixed issue #316, top_marker()
• Fixed issue #346, find_gene_modules()

monocle3 0.2.2

Changes

• 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().

Bug fixes

• 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).

monocle3 0.2.0

Major changes

• 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().

Other Changes

• Added non-standard color options for plot_cell_3d.
• Added norm_method = 'none' option for importing pre-normalized data.

Bug fixes

• 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.

monocle3 0.1.3

Changes

• 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.

Bug fixes

• 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.

monocle3 0.1.2

Changes

• Added a NEWS.md file 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.

Bug fixes

• Fixed a bug that made expression matrix the wrong class with load_cellranger.