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Visiumhd #45

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andpet0101
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This PR introduces all neccessary changes for the analysis of VisiumHD datasets. In addition, it includes changes required for the analysis of multiple assays.

  • Added a 10x VisiumHD dataset
  • Added functions for reading 10x VisiumHD counts and images
  • The assay type is now included in the names of dimensionality reductions, visualizations, graphs and clusterings. This is a requirement for analysing VisiumHD and other multi-assay datasets.
  • Code of the modules was updated accordingly. Mostly this means making sure that only the default assay is analysed.
  • Improved the readability for the modules dimensionality_reduction and clustering_umap so that it is better to understand (better variable names, more comments and documentation).
  • Smaller fixes that were found during the tests

We can also discuss this one as well. It looks much but most of it is just optimisation and better code. I tried hard.

@andpet0101
Added Visium HD dataset
a997c73
@andpet0101
Introduced function for reading 10x VisiumHD counts. Restructed creat…
abd9375 
…ing the Seurat object so that assays can add new barcodes
@andpet0101
Import of VisiumHD images
6bdcfa2
@andpet0101
Updated the qc_filtering module for VisiumHD. Added spatial plots for…
aeebf83 
… filtered cells.
@andpet0101
Updated normalization module
5df1a74
@andpet0101
Dimensionality reductions now include the assay name
52a3296
@andpet0101
Updated clustering_umap module
e8895d1
@andpet0101
Updated clusterqc module
63e3a2f
@andpet0101
Updated cluster_annotation module
fe8519d
@andpet0101
Updated cluster_composition module
501de72
@andpet0101
Restructured IntegrateLayersWrapper function. Made scVIIntegration_Fi…
0efabd9 
…xed function work again.
@andpet0101
Restructed creating the Seurat object again so that assays can add ne…
7daeb9c 
…w barcodes.

- The changes introduced in commit abd9375 were not sufficient enough to allow multiple assays as well as multiple samples. This should fix it.
@andpet0101
Allow filtering of barcodes from individual assays so that they are s…
e1a5dbf 
…till kept in other assays
@andpet0101
Changes to the way parameters are parsed for the integration methods
3a0bff0
@andpet0101
Merge branch 'main' into visiumhd, resolved conflicts and adjusted fo…
28c7495 
…r visiumhd branch
@andpet0101
Improved readability of the code regarding assay, dimensionality redu…
58f0c04 
…ction, sketching
@andpet0101
Updated export code to deal with only a specific assay
344e638
@andpet0101
Updated ExportLoupe and ExportXeniumExplorer functions to export only…
32ec1fe 
… a specific assay
@andpet0101
Last small fixes before merge request.
97071e4
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@ktrns ktrns Awaiting requested review from ktrns

@rajinder4489 rajinder4489 Awaiting requested review from rajinder4489

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@andpet0101