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Support to handle .parquet output from Vizgen #7190

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Commits on Apr 13, 2023

  1. updates for Vizgen

    alikhuseynov committed Apr 13, 2023
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  2. updates for Vizgen

    alikhuseynov committed Apr 13, 2023
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  3. updates for ReadVizgen()

    alikhuseynov committed Apr 13, 2023
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  4. updates for LoadVizgen

    alikhuseynov committed Apr 13, 2023
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  7. fix args for ReadVizgen

    alikhuseynov committed 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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  2. fix for LoadVizgen

    alikhuseynov committed May 31, 2023
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Commits on Jun 6, 2023

  1. major fix for ReadVizgen()

    ..reads old-new data, optimized parallelization, few bugs fixed
    alikhuseynov committed Jun 6, 2023
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  2. fix for LoadVizgen()

    ..supports args:
    `mol.type`, `filter`, `z`
    added `verbose` for optional verbosity
    alikhuseynov committed Jun 6, 2023
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Commits on Jul 26, 2023

  1. update ReadVizgen()

    ..resolve some small conflict for 
    `Read10X_Image()`
    alikhuseynov committed Jul 26, 2023
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  2. update LoadVizgen()

    ..adding of molecules to the object is optional `add.molecules = TRUE`
    alikhuseynov committed Jul 26, 2023
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Commits on Aug 18, 2023

  1. cleaning ReadVizgen

    few small edits for cleaner code.
    alikhuseynov committed Aug 18, 2023
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Commits on Aug 22, 2023

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Commits on Aug 28, 2023

  1. 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)
    alikhuseynov committed Aug 28, 2023
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  2. ..updated LoadVizgen()

    alikhuseynov committed Aug 28, 2023
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  4. optimized parallelization for .filter_polygons()

    ..optimized parallelization `BiocParallel` for 
    `.filter_polygons()`, ie using 2 workers less that total provided workers
    alikhuseynov committed Aug 28, 2023
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Commits on Feb 15, 2024

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