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How to use totalVI denoised protein measurements
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1
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61
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November 9, 2025
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Question about get_normalized_expression computation
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3
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118
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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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138
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November 4, 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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142
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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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47
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October 10, 2025
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Is Gaussian mixture VAE implemented in scVI-tools?
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3
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79
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September 25, 2025
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Preprocess of scATAC use for peakVI or MultiVI
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5
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182
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September 3, 2025
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Using ResolVI’s Unsupervised Mode for Cell Annotation
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7
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391
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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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75
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August 19, 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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126
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August 5, 2025
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Conduct SCANVI after running SysVI on multi-platform data
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3
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72
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August 3, 2025
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Unexpected DE test results in scvi version 1.3.0 (as compared with version 1.1.2)
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15
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392
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July 31, 2025
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Implementing Warmup to a component based on epoch
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2
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75
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July 31, 2025
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Error when trying to use scvi.model.SCANVI.from_scvi_model
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7
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343
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July 22, 2025
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Problems with Bayes factors and LFC changes using model.differential_expression()
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8
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301
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July 9, 2025
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Wrong log-fold change estimation?
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3
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97
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July 9, 2025
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Discrepancy between raw mean/non-zero proportion and LFC with model.differential_expression
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2
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103
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July 10, 2025
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Does MultiVI support using tile matrix directly instead of peak calling for ATAC input?
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2
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89
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July 9, 2025
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The best practice for detecting differential gene expression between 2 types of samples
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4
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1113
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July 9, 2025
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Documentation for training with multiple GPUs
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5
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451
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July 9, 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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229
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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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107
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June 19, 2025
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Workflow advice for totalVI in CITE-seq Multiplexed data
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3
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153
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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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255
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May 27, 2025
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Amortized LDA Topic Modeling - picking the right number of topics
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8
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222
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June 4, 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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220
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June 3, 2025
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Help on MultiVI for data modality
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1
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252
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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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655
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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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249
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May 11, 2025
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Nan values in the latent of scanvi_query
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1
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66
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April 23, 2025
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