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Predict cell type with scANVI for spatial transcriptomics data (Xenium)
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6
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103
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November 27, 2025
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Question about complex experiment
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1
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46
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November 25, 2025
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Pseudobulk after Performing integration with scatlasvae or scVI?
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1
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51
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November 6, 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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85
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October 22, 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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53
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October 7, 2025
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Anchor-based integration methods
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1
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51
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September 25, 2025
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How to Correct for Intra-Organ Batch Effects Without Removing Inter-Organ Differences?
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6
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92
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August 5, 2025
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Can we use resolVI and squidpy to annotate a CosMX object based on a single cell reference?
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1
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86
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August 3, 2025
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How to handle batch effects within the query dataset when using scArches + SCVI?
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1
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86
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July 31, 2025
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Shared cell types not mixing when integrating datasets from different species
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4
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173
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June 19, 2025
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SMART-seq and MARS-seq pipelines
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1
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79
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June 19, 2025
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Domain adaptation to pre-train batch correction model using paired data
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12
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202
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May 27, 2025
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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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179
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June 3, 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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48
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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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351
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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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93
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April 10, 2025
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inferCNVpy after running scVI with batch as key
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5
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920
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March 24, 2025
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Error when running scvi.data.add_dna_sequence
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1
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74
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March 18, 2025
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SysVI model and normalized expression
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1
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142
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March 15, 2025
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Scvi-tools and xenium
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7
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673
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March 13, 2025
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Parameters in training model for integrating datasets with scVI in R
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13
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157
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March 9, 2025
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TotalVI not fully integrating CITEseq cells with GEX and missing protein values
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1
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85
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February 6, 2025
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What training datasets are used in the scVI pretrained model (version 2024-07-01)?
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2
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101
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December 23, 2024
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What kind of data type does infercnvpy need as input?
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0
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59
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November 27, 2024
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scVI: effect of unbalanced number of cells in batches
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1
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111
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November 27, 2024
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Scvi-tools: different DEGs when comparing same data
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2
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160
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November 19, 2024
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How to best integrate scRNA-seq with transcription factor expression measured by fluorescent signals
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0
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51
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November 18, 2024
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Integrating different tissues with scVI
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3
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225
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November 15, 2024
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scVI 21618 problem
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5
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332
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November 7, 2024
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[suggestion] what would be the appropriate pipeline to perform joint embedding of GEX and ATAC?
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1
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110
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October 17, 2024
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