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Support to handle .parquet
output from Vizgen
#7190
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alikhuseynov
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Commits on Apr 13, 2023
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Commits on Apr 19, 2023
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Commits on May 24, 2023
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Commits on May 31, 2023
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Commits on Jun 6, 2023
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..reads old-new data, optimized parallelization, few bugs fixed
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..supports args: `mol.type`, `filter`, `z` added `verbose` for optional verbosity
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Commits on Jul 26, 2023
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..resolve some small conflict for `Read10X_Image()`
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..adding of molecules to the object is optional `add.molecules = TRUE`
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Commits on Aug 18, 2023
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Commits on Aug 22, 2023
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Commits on Aug 28, 2023
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added
sf
& filter polygons ->ReadVizgen()
..inspired by [`SpatialFeatureExperiment`](https://github.com/pachterlab/SpatialFeatureExperiment) using`sf` package to work/filter segmentation geometries. Updates: - adding support to efficiently filter segmentation polygons (removing small artifacts etc..) - added helper function `.filter_polygons()` (a bit modified version from `SpatialFeatureExperiment:::.filter_polygons`) for filtering given `min.area` - minimal polygon area as a threshold - allow for multiple segmentation polygons per cell (..still using single z-plane)
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optimized parallelization for
.filter_polygons()
..optimized parallelization `BiocParallel` for `.filter_polygons()`, ie using 2 workers less that total provided workers
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Commits on Feb 15, 2024
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