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Orian bioconductor3 20 updates #39

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  • Updated SpaceMarkersVersion
  • Updated SpaceMarkersMetric by fixing signage and log transformed to scale
    magnitude
  • Added getSpatialParameters_External which enables getting spatial parameters
    from file or from the user
  • Enabled includeSelf = TRUE in getInteractingGenes.R to improve hotspot
    detection
  • Enabled preprocessing.R to read expression and coordinates from VisiumHD

…nd transformed the SpaceMarkersMetric with log2(abs()+1) to prevent skewing of the scale. Updated Package version
…ders the spatial pattern itself in calculating influence instead of only considering the spots around it. Updated default kernel threshold to be slightly more stringent since more hotspots will be produced. Updated Package version
…ecify sigma for kernel width for smoothing and outlier threshold for hotspots. The default behavior is to pull the spot diameter from a 10xVisium .json file from the usual spatial folder created by Visium.
…xpr to read expression from VisiumHD which are stored in .parquet files. Added the nanoparquet function to depends in DESCRIPTION as well as updated package version. Updated NEWS.md
@orian116 orian116 closed this Oct 14, 2024
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