NEWS.md

scKirby 0.1.5

New features

• Move more functions from phenomix --> scKirby:
  • compute_cor --> calc_cor
  • compute_snn
  • create_DimReducObject
  • get_cor
  • has_graph
  • infer_graph_name --> infer_graph_key
  • normalise
  • yeojohnson
  • is_installed
• dict_class
  • Add "Graph" to "matrix" class.
• New exported functions:
  • set_obsp
  • to_delayedarray

scKirby 0.1.4

New features

• Rename get_data --> get_x to align with anndata nomenclature and avoid conflicts with piggyback-oriented functions.
• is_class
  • Add new classes: "matrix_strict", "matrix_sparse", "delayed_array"

• get_x
  • Add new args slot and assay
• New funcs:
  • get_obs_names
  • get_var_names
  • mofa_to_dimreduc
• get_obsm: can now handle MOFA models.
• get_varm: can now handle MOFA models.
• get_obs/ get_var can now take matrices.
• is_class:
  • Now recognises class "matrix_list"

scKirby 0.1.3

New features

• anndata_to_ctd:
  • New function to create CTD by chunking anndata obj.
• seurat_to_anndata
  • Add support for anndataR method.

Bug fixes

• map_data
  • Change default: as_sparse=TRUE

scKirby 0.1.2

New features

• Move scNLP::seurat_pipeline --> scKirby::process_seurat
  • New subfunction calc_specificity

scKirby 0.1.1

• Implemented rworkflows
• Added a NEWS.md file to track changes to the package.