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Changelog

Source: NEWS.md

SeuratIntegrate (development version)

  • Fix AnnData initialization: the var argument for features is now a data.frame

  • Fix overestimation of number of zeros in sparse matrices: remaining 0s in the matrix values are discarded before counting non-zero values (src/n_zeros_matrix.cpp)

  • Fix choose_matrix_format() (utils.R)

  • Created a first set of unit tests covering utils.R (testthat)

  • Add method to preserve a Graph object’s attributes when using as.Graph on a Graph object

  • Fix deprecation warning in GetNeighborsPerBatch (Graph method)

  • Minor fixes in docstrings

SeuratIntegrate 0.4.1

  • Revised score rescaling with a new option enabling min-max rescaling of ranks (default) rather than scores directly (as in Luecken et al., 2021)

  • Speed up Dijkstra’s algorithm-like used in ExpandNeighbours with a new c++ implementation

  • The most suited matrix format is automatically chosen for corrected counts output by integration methods (should be dense matrix most of the time)

  • Add support for scGraph metric (Wang et al., 2024)

  • Improved speed of CreateIntegrationGroups for non-SCT assay in unambiguous cases

SeuratIntegrate 0.4.0

  • Initial public release