Accelerated, Python-only, single-cell integration benchmarking metrics
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Oct 28, 2026 - Python
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scvi-tools
Here are 33 public repositories matching this topic...
Notebooks used in scvi-tools tutorials
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Oct 28, 2026 - Jupyter Notebook
Template repository for creating novel models with scvi-tools
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Jan 18, 2023 - Python
scVIVA-Tools: A unified toolkit for spatial transcriptomics analysis
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Oct 28, 2026 - Python
Deep Learning Based Models for Preimplantation Mouse and Human Development
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Jan 17, 2025 - Jupyter Notebook
Sobolev alignment of deep probabilistic models for comparing single cell profiles
python deep-learning clinical gene-expression cancer-genomics scrna-seq single-cell variational-autoencoder cell-lines scanpy pre-clinical kernel-machine-learning drug-response scvi-tools
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Oct 26, 2026 - Python
Variational Inference for Cell Type Evolution
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Apr 18, 2026 - Jupyter Notebook
MCP (Model Context Protocol) server for deep probabilistic analysis of single-cell omics data using scvi-tools
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Oct 28, 2026 - Python
Lightweight helper to install scvi-tools in Google Colab
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Oct 28, 2026 - Python
scRNA Analysis tutorials
python bioinformatics r tutorials bioinformatics-pipeline transcriptomics bioinformatics-analysis single-cell-rna-seq seurat bulk-rna-seq scanpy scvi-tools
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Jan 23, 2023 - HTML
Single-cell RNA-seq analysis of mouse gastrulation using data from Argelaguet and Pijuan-Sala. The project includes preprocessing, SCVI-based dataset integration, differential gene expression analysis, and a no-code interface powered by Chatmol for natural language interaction with the pipeline.
python bioinformatics deep-learning gpu-acceleration dimensionality-reduction scrna-seq data-integration llama single-cell differential-expression umap developmental-biology no-code embryogenesis scanpy gastrulation anndata scvi-tools mouse-development
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Jun 1, 2025 - Jupyter Notebook
A variational autoencoder (VAE) for joint inference of cyclical dynamics and cellular state from single-cell RNA-seq data
pytorch single-cell circular-statistics variational-inference latent-variable-models rna-velocity scvi-tools
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Oct 10, 2026 - Python
Cross-species (human/mouse) islet scRNA-seq integration over a 1:1 ortholog gene space, with a from-scratch VAE and scVI. A learning project.
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Sep 10, 2026 - HTML
Code for the MiSTR microfluidic stem cell atlas study of early human neural patterning.
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Mar 2, 2026 - Jupyter Notebook
Sparse autoencoders on scVI latent space of the BoneMarrowMap haematopoietic atlas: functional programme discovery, RAG-LLM annotation, cross-lineage FP-Tree and progenitor commitment
computational-biology single-cell sparse-autoencoders scvi-tools scvi mechanistic-interpretability llm-annotation haematopoiesis
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Oct 17, 2026 - HTML
Cross-cohort cell-type annotation of colorectal cancer scRNA-seq with scVI and scANVI: open-set novelty, calibration and conformal coverage under cohort and hospital shift
bioinformatics deep-learning pytorch calibration scrna-seq transfer-learning single-cell uncertainty-quantification model-evaluation conformal-prediction novelty-detection scanpy anndata cell-type-annotation colorectal-cancer scvi-tools label-transfer scanvi scarches
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Oct 27, 2026 - Python
Single-cell RNA-seq analysis of ~100k lung cells: Scanpy, scVI integration, cell-type annotation and CellChat signalling
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Oct 6, 2026 - Jupyter Notebook
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