scRNA-seq

• Atlas-level integration of lung data
• MrVI Quick Start Tutorial
• Benchmarking the scANVI fix
• Seed labeling with scANVI
• Integration and label transfer with Tabula Muris
• Differential expression on C. elegans data
• Annotation with CellAssign
• Isolating perturbation-induced variations with contrastiveVI
• Linearly decoded VAE
• Topic Modeling with Amortized LDA
• Identification of zero-inflated genes
• Integration of scRNA-seq data with substantial batch effects using sysVI
• Decipher Quick Start Tutorial
• Variational inference for RNA velocity with VeloVI
• MrVI analysis over Tahoe100M cells dataset

Atlas-level integration of lung data

Perform integration of multiple scRNA-seq datasets both with and without cell type annotation (scVI and scANVI)

scRNA-seq

MrVI Quick Start Tutorial

Analyze multi-sample scRNA-seq data with MrVI in Jax

scRNA-seq

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Analyze multi-sample scRNA-seq data with MrVI in PyTorch

scRNA-seq

Benchmarking the scANVI fix

Compare scANVI to other models following a bug fix in scvi-tools 1.1.0

scRNA-seq

Seed labeling with scANVI

Create seed labels and transfer cell type annotations to an entire dataset

scRNA-seq

Integration and label transfer with Tabula Muris

Perform de novo integration of a labeled reference dataset with an unlabeled query dataset (label transfer)

scRNA-seq

Differential expression on C. elegans data

Perform DE analysis on C. elegans data with scVI to quantify differences in gene expression between groups of cells

scRNA-seq

Annotation with CellAssign

Use CellAssign to assign cell types using only knowledge of marker genes

scRNA-seq

Isolating perturbation-induced variations with contrastiveVI

Use contrastiveVI to isolate perturbation-induced variation in Perturb-seq data

scRNA-seq

Linearly decoded VAE

Fit an LDVAE model to scRNA-seq data and interpret how genes are linked to latent variables of cells

scRNA-seq

Topic Modeling with Amortized LDA

Run the amortized Latent Dirichlet Allocation model in scvi-tools to learn topics of an scRNA-seq dataset

scRNA-seq

Identification of zero-inflated genes

Use the AutoZI model to enable gene-specific treatment of zero-inflation

scRNA-seq

Integration of scRNA-seq data with substantial batch effects using sysVI

Integrate scRNA-seq datasets with substantial batch effects.

scRNA-seq

Decipher Quick Start Tutorial

Use Decipher to jointly analyze samples from distinct conditions.

scRNA-seq

Variational inference for RNA velocity with VeloVI

Use VeloVI to estimate RNA velocity.

scRNA-seq

MrVI analysis over Tahoe100M cells dataset

Analyze Tahoe100M cells dataset with MrVI in PyTorch

scRNA-seq

Notebook not found, path tried: /home/docs/checkouts/readthedocs.org/user_builds/scvi/checkouts/stable/docs/tutorials/notebooks/scrna/Tahoe100_mrVI_Jax.ipynb

Analyze Tahoe100M cells dataset with MrVI in Jax

scRNA-seq