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Impact of scaling on clustering results and controlling minimum cluster size in Leiden clustering
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1
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102
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November 10, 2025
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How should I process the data after removing low-quality cell clusters?
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0
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35
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November 9, 2025
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How to use totalVI denoised protein measurements
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1
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49
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November 9, 2025
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Rank_genes_groups expects log data but default to adata.raw, why?
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0
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51
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November 7, 2025
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Convert Scanpy (h5ad) to Seurat (rds)
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10
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17659
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November 6, 2025
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Question about get_normalized_expression computation
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3
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88
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November 5, 2025
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Batch key and categorical variables for get_normalized_expression()
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2
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108
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November 4, 2025
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Same scVI model with different values on mac silicon and linux?!
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1
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47
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November 4, 2025
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Question about implementation of highly_variable_genes
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0
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34
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November 3, 2025
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Calculate gene signature scores from cell2location-deconvolved spatial transcriptomics
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0
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23
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October 22, 2025
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Pathway quantification with decoupler - questions on the possible inputs
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3
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85
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October 22, 2025
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Excluding Ig and ribosomal genes from HVG selection in scVI, best practice?
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1
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101
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October 22, 2025
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Potential bug in scvi.model.TOTALVI.setup_mudata
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2
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45
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October 10, 2025
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Changing the order of the anndata objects in anndata.concat changes the leiden clustering
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6
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108
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October 9, 2025
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Infercnvpy | get positional information for bins
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0
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37
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October 7, 2025
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Help with package setup
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2
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42
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October 7, 2025
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How to use scib benchmark-metrics evaluate the adata after BBKNN integretion
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3
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71
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October 7, 2025
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Is Gaussian mixture VAE implemented in scVI-tools?
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3
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69
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September 25, 2025
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Anchor-based integration methods
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1
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57
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September 25, 2025
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Posterior probability interpretability (soft=True)
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1
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60
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September 25, 2025
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Cell charter niche calling
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5
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309
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September 13, 2025
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Preprocess of scATAC use for peakVI or MultiVII
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2
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21
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September 16, 2025
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Preprocess of scATAC use for peakVI or MultiVI
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5
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156
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September 3, 2025
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Memory Usage in multiple New Formats
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2
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107
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September 2, 2025
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How can I operate on view of Anndata object when the Object itself is large to load to memory?
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1
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97
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September 2, 2025
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Error ir.tl.summarize_clonal_expansion
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2
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27
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September 2, 2025
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multiVI speed and cpu consumption
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2
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70
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August 30, 2025
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Using ResolVI’s Unsupervised Mode for Cell Annotation
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7
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244
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August 26, 2025
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Get_normalized_expression causes my kernel to disconnect
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1
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51
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August 19, 2025
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Decoupler error: raw input data has integers, will not accept "skip_checks=True"
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1
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41
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August 19, 2025
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