CHANGELOG.md

In kharchenkolab/scITD: Single-Cell Interpretable Tensor Decomposition

Upcoming

[1.0.4] - 2023-09-06

Changed

• Added a catch and correction for special characters present in cell type names
• Removed ssvd dependency and sparse tucker implementation
• Updated readme to include instructions for installing other dependencies
• Fixed error in LR analysis caused by genes with 0 expression

[1.0.3] - 2023-01-23

Added

• New function for users to easily get gene significance p-values for a factor
• Additional url for new LR analysis tutorial in the README

Changed

• Enabled compute_LR_interact to run when data contains alternate gene symbols
• Included warning/catch in plot_loadings_annot if no genes are significant
• Fixed bug in determine_ranks_tucker with variance scaling in wrong order
• Updated README figure

[1.0.2] - 2022-03-23

Added

• Added count_word() function from simplifyEnrichment package as the remoevd it
• Included necessary suggests packages for count_word()

Changed

• Updated README to include our preprint citation and new figure

[1.0.1] - 2022-01-28

Added

• Optional parameters min_gs_size and max_gs_size to run_gsea_one_factor()
• New function project_new_data() to project a multicellular pattern onto new data
• Warning if cell-level metadata is included as donor-level metadata
• Check that cell type names in ctypes_use are spelled correctly

Changed

• Checks for empty batches before running ComBat batch correction
• Fixed label issue with LR output when only have associations with 1 factor

[1.0.0] - 2021-10-08

Added

• Option to use custom list of genes in the tensor
• Check for matching cell names between count matrix and metadata

Removed

• Removed optimize_var_scale_power() and helpers as they're no longer used
• Removed compare_factors() and helpers as they're no longer used

Changed

• Fixed anova vargenes method for genes with zero expression across donors
• Updated run_jackstraw() and get_min_sig_genes() to work with new rotations
• Fixed bug in plot_subclust_associations()
• Enabled storage of results from get_subtype_prop_associations()
• Updated README to no longer require dev version of ComplexHeatmap
• Updated DESCRIPTION authors and description

kharchenkolab/scITD documentation built on Sept. 25, 2023, 11:02 p.m.