NEWS

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SuperCellCyto 0.99.3

• Update vignettes for interoperability with sce to create sce object within rather than loading from qs2 object.
• Removed sce q2 object from inst/extdata.

SuperCellCyto 0.99.2

• Moved data for vignettes to inst/extdata and update vignettes accordingly.
• Added scripts to generate files in inst/extdata and a README to inst folder.
• Updated qs object for vignettes to qs2 object.
• Minor change in runSuperCellCyto to use sprintf to print warning message.

SuperCellCyto 0.99.1

• Changed paste to sprintf for warning messages.
• Moved example data to inst/extdata and update vignettes.
• Add chunk labels to vignettes.

SuperCellCyto 0.99.0

Major changes

• Added support to use median when recomputing supercells.
• Introduced n_pc parameter to allow users to specify the number of principal components to use in the PCA step when computing supercells.
• Added utils.R file to contain utility functions that are commonly used.

Minor changes

• Cleaned up functions and added improvements to the codebase, in accordance with the Bioconductor package development guidelines.
• Updated vignettes to BiocStyle.
• Added more tests.

SuperCellCyto 0.1.0

This is the first release of SuperCellCyto.

This is also the version of SuperCellCyto that was used in our preprint:

@article{
    putri2023supercellcyto,
    title={SuperCellCyto: enabling efficient analysis of large scale cytometry datasets},
    author={Putri, Givanna H and Howitt, George and Marsh-Wakefield, Felix and Ashhurst, Thomas Myles and Phipson, Belinda},
    journal={bioRxiv},
    pages={2023--08},
    year={2023},
    publisher={Cold Spring Harbor Laboratory}
}