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scVI batch correction clusters all cells from sample in a circle (potential artifact)
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14
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96
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June 3, 2025
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Popv AssertionError: Don’t call _normalize_index with non-categorical/string names
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1
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47
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May 31, 2025
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Macbook M1 M2 mps acceleration with scVI
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9
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1655
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May 30, 2025
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Lazy Loading Anndata backed in Zarr Arrays from Disk
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5
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97
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May 28, 2025
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Efficient pseudobulking
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4
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133
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May 28, 2025
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Unexplained change in UMAP
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3
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76
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May 27, 2025
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Spatialdata.aggregate, image and segmentation_mask have different shape, but aligned in 'global'
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1
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39
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May 26, 2025
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Sc.pp.highly_variable_genes with batch_key causes segmentation fault
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2
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224
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May 26, 2025
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Good spatial tutorial for beginners
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3
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138
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May 21, 2025
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Preprocessing CITE-seq with muon
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0
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25
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May 19, 2025
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Help on MultiVI for data modality
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1
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192
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May 16, 2025
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Protocol for model optimization (currently focused on MultiVI)
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3
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552
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May 14, 2025
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How to interpret reconstruction loss increase but elbo loss decrease on trained scvi and scanvi models
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1
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67
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May 11, 2025
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Convert anndata to seurat (spatial)
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1
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89
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May 9, 2025
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Mu.pp.intersect_obs()
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7
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118
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May 9, 2025
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Nan values in the latent of scanvi_query
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1
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19
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April 23, 2025
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Modify gene identifiers stored in existing scVI model
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1
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31
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April 20, 2025
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Anndata Manager Store
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11
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65
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April 20, 2025
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Scvi package can't be installed into google colab?
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6
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47
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April 20, 2025
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How to retreive the V,D,J gene segment idenifiers and CD3 sequence give a clone_id?
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1
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21
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April 18, 2025
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Is the scVI model applicable to bulk RNA-seq data from cell lines?
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1
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66
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April 16, 2025
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Memory Usage in multiple New Formats
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0
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27
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April 13, 2025
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Best Practices for Multi-Panel Figures
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0
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41
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April 11, 2025
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How to transfer annotation from cell subset to original object?
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1
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45
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April 10, 2025
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How to plot annotation in Xenium data using spatialdata
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8
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117
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April 10, 2025
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How should I calculate the knn entropy using the leiden clusters?
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1
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26
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April 10, 2025
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Understanding scVI integration inside R with Seurat v5 & SCTransform
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1
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185
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April 6, 2025
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How to fix number of nodes used in HPC environment with scvi.train (via R & reticulate)?
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8
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49
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April 10, 2025
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Stacked violin API related question
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2
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369
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April 1, 2025
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Any MLX (MPS) framework accelerate solution for scanpy？
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1
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62
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March 31, 2025
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