v4.1.0 #1003
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v4.1.0 #1003
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--- TODO: - instructions on dbMatrix installation - subsequent steps in Giotto workflow
…malization workflow --- TODO: - update custom normalization workflows. - add proper setters from dbMatrix
sync suite
Modular reader class implementation for CosMx outputs
feat: add cosmx reader proto
- Fix stats::density and GiottoClass::density naming overlap - document
fix: namespace issue
chore: improve docs
fix: catch empty condition of cosmx_dir
- add micron scaling - make naming align with nanostring standards - add image name parsing for FOV number - use individual params instead of param lists for clarity - change fov shifts detection to mainly being derived from metadata or transcripts instead of loading the values in since they are usually in micron scaled values.
- add progressr for FOV-specific operations
- add debug message with path
feat: dbverse integration --- filterGiotto() normalizeGiotto()
feat: xenium convenience update
image_register&segment
Add: three functions for ONTraC integration
- `performCellposeSegmentation()` -> `doCellposeSegmentation()`
chore: naming change and document
chore: update news
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Breaking changes
detectSpatialCorGenes()removed. UsedetectSpatialCorFeats()insteadfindInteractionChangedGenes()removed. UsefindInteractionChangedFeats()insteadfindCellProximityGenes()removed. UsefindInteractionChangedFeats()insteadcreateGiottoXeniumObject()has been overhauled and parameters have changed.Bug fixes
plotInteractivePolygons()when providing a spatial plot with a continuous scale #964 by jweis3find_dampening_constant()whenS[subset, ]produces only 1 gene.interpolateFeatures()where feature names with-or starting with numbers did not workrunPCAprojectionBatch()for when ncp requested exceeds number of feats usedspatCellCellcom()respectverboseflag #949 by rbutleriiiNew
read10xAffineImage()for reading 10x affine transformed imagesEnhancements
print()methods foricfObjectandcombIcfObjectChanges