Accelerated, Python-only, single-cell integration benchmarking metrics
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Sep 22, 2026 - Python
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scvi-tools
Here are 27 public repositories matching this topic...
Notebooks used in scvi-tools tutorials
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Sep 21, 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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Sep 22, 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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Sep 21, 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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Sep 21, 2026 - Python
Lightweight helper to install scvi-tools in Google Colab
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Sep 21, 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
Reproducible ImmGenT T-cell reference integration pipeline
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Aug 14, 2026 - Python
Code for the MiSTR microfluidic stem cell atlas study of early human neural patterning.
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Mar 2, 2026 - Jupyter Notebook
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
FAIR single-cell RNA-seq pipeline mapping nerve–tumour–immune ligand–receptor crosstalk in glioblastoma across 170 donors (CELLxGENE Census, two sequencing-depth arms). Compartment integrity enforced as build gates against a held-out annotation. Snakemake + scvi-tools + scanpy + LIANA + marimo.
bioinformatics snakemake scrna-seq single-cell fair-data glioblastoma immuno-oncology scanpy ligand-receptor cellxgene scvi-tools liana marimo neuro-oncology cancer-neuroscience
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Sep 12, 2026 - Python
Reproducible single-cell framework for immune aging using scVI, donor-aware analyses, molecular signatures, and age prediction.
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Aug 31, 2026 - Python
Reproducible benchmark of four scRNA-seq cell type annotation methods (SingleR, CellTypist, ACTINN, scANVI) on PBMC3K
benchmark bioinformatics scrna-seq bioinformatics-analysis scrna-seq-data single-cell-rna-seq single-cell-analysis scrna-seq-analysis single-cell-sequencing pbmc singler actinn scvi-tools pbmc3k celltypist
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Aug 7, 2026 - Jupyter Notebook
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