Version 3.1.4

Fixes normalizeCounts(..., method = "SCT").

Version 3.1.3

Fixes:

• Website tutorials

Adds:

• removeSignatures()

Version 3.1.2

Fixes:

• runBayesSpaceClustering()

Version 3.1.1

Changes:

• Fixes flipAll().
• Fixes plotSurfaceInteractive().

Version 3.1.0

Changes:

• Fixes spatialTrajectoryScreening() in case of missing capture areas.
• Improved precision in computing the capture area of Visium Experiments.
• Fixes bad polygon display in case of ggpLayerSpatAnnOutline() with expand_outline = 0.
• Improved options and comfort in createSpatialSegmentation().

Additions:

• reduceResolutionVisiumHD() to create SPATA2 objects with individual VisiumHD resolution beyond the standard (16um, 8um and 2um).
• resizeImage() for memory friendly handling of large images.

Version 3.0.3

Changes:

• fixes initiateSpataObjectVisium() for different chemistry versions of 10X
• introduces reduceResolutionVisiumHD() and individual adjustment of resolution during initiation with initiateSpataObjectVisiumHD()

Version 3.0.2

Changes:

• fixes normalizeCounts()

Version 3.0.1

Changes:

• fixes identifyTissueOutline(..., method = "image")
• updates documentation
• updates tutorials

Additions:

• reduceResolutionVisiumHD()
• ggpLayerGridVisiumHD()

Version 3.0.0

The release of SPATA2 v3.0.0, coinciding with the official publication of SPATA2:

Kueckelhaus, J., Frerich, S., Kada-Benotmane, J. et al. Inferring histology-associated gene expression gradients in spatial transcriptomic studies. Nat Commun 15, 7280 (2024). https://doi.org/10.1038/s41467-024-50904-x

Version 2.0.4

Changes:

• Fixes asSPATA2() for Giotto.
• Fixes order in which to install the packages in the article on how to install the package.
• Fixes article on image handling.
• Changes default clrp to 'sifre'. (Can always be changed with setDefault(object, pt_clrp = "...", clrp = "...") )
• Splits setTissueOutline() in identifyTissueSections() and identifyTissueOutline()

Additions:

• Uploads the tutorial on platform compatibility.