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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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135
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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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46
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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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78
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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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178
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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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369
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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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125
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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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390
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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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73
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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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337
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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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296
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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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96
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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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100
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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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88
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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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1108
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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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444
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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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226
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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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106
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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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150
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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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251
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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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219
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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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217
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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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250
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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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651
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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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240
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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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64
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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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61
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April 20, 2025
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Anndata Manager Store
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11
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193
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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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131
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April 20, 2025
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