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Orian bioconductor3 20 updates #39

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wants to merge 4 commits into from
Closed

Orian bioconductor3 20 updates #39

wants to merge 4 commits into from

Commits on Oct 14, 2024

  1. Updated getSpaceMarkersMetric to Include AND in Zsign instead of OR a… 

    …nd transformed the SpaceMarkersMetric with log2(abs()+1) to prevent skewing of the scale. Updated Package version
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    orian116 committed Oct 14, 2024
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  2. Update to find_pattern_hotspots for includeSelf=TRUE. This mode consi… 

    …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
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  3. Added a getSpatialParametersExternal function to allow the user to sp… 

    …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.
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  4. Updated load10XCoords to be able to read tissue positions and load10E… 

    …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
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