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CHANGELOG.md

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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