# 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.
