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    75 repositories

    • scib-metrics

      Public
      Accelerated, Python-only, single-cell integration benchmarking metrics
      deep-learningscvi-toolsscib
      deep-learningscvi-toolsscibscversesinglecell-data-analysis
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •22•98•2•5•Updated Oct 20, 2026Oct 20, 2026

    • scvi-tools-mcp

      Public
      MCP (Model Context Protocol) server for deep probabilistic analysis of single-cell omics data using scvi-tools
      mcpagentssinglecell
      mcpagentssinglecellspatial-transcriptomicsscvi-toolsscversellmagentskills
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Oct 20, 2026Oct 20, 2026

    • scviva-tools

      Public
      scVIVA-Tools: A unified toolkit for spatial transcriptomics analysis
      deep-learningspatial-transcriptomicsscvi-tools
      deep-learningspatial-transcriptomicsscvi-toolsscversescviva-tools
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•15•0•5•Updated Oct 20, 2026Oct 20, 2026

    • treedata

      Public
      anndata with trees
      data-sciencebioinformaticsscanpy
      data-sciencebioinformaticsscanpyanndatalineage-tracingscverse
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•9•0•1•Updated Oct 19, 2026Oct 19, 2026

    • destvi_utils

      Public
      Utilities for downstream analysis of destVI
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•1•1•Updated Oct 19, 2026Oct 19, 2026

    • mrvi_archive

      Public
      Multi-resolution Variational Inference
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•24•2•1•Updated Oct 19, 2026Oct 19, 2026

    • popV

      Public
      Python
      •
      MIT License
      •20•102•7•2•Updated Oct 19, 2026Oct 19, 2026

    • pycea

      Public
      scverse lineage tracing analysis toolkit
      bioinformaticsscanpylineage-tracing
      bioinformaticsscanpylineage-tracingtreedatascverse
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•5•0•0•Updated Oct 8, 2026Oct 8, 2026

    • treedataR

      Public
      Read/Write TreeData Objects
      R
      •
      Other
      •0•0•0•0•Updated Oct 6, 2026Oct 6, 2026

    • scviva-legacy

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 5, 2026Oct 5, 2026

    • scviva-tools-website

      Public
      website for scVIVA-Tools
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•5•Updated Sep 21, 2026Sep 21, 2026

    • csde

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•12•2•0•Updated Sep 1, 2026Sep 1, 2026

    • Cassiopeia

      Public
      A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
      computational-biologycrispr-cas9single-cell-rna-seq
      computational-biologycrispr-cas9single-cell-rna-seqlineage-tracingsingle-cell-lineage-tracingcomputational-phylogenetics
      Python
      •
      MIT License
      •32•101•15•2•Updated Jul 23, 2026Jul 23, 2026

    • yoseflab.github.io

      Public
      JavaScript
      •
      MIT License
      •9•3•0•0•Updated Jul 8, 2026Jul 8, 2026

    • Harreman-reproducibility

      Public
      Reproducibility repository for the Harreman manuscript.
      Jupyter Notebook
      •0•0•0•0•Updated Jul 8, 2026Jul 8, 2026

    • visionpy

      Public
      Functional interpretation of single cell similarity maps
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •4•6•0•3•Updated Jun 30, 2026Jun 30, 2026

    • VIVS

      Public
      Calibrated Identification of Feature Dependencies in Single-cell Multiomics
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•5•1•1•Updated Jun 22, 2026Jun 22, 2026

    • Harreman

      Public
      Harreman infers metabolic exchanges in tissues using spatial transcriptomics.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•11•0•0•Updated May 11, 2026May 11, 2026

    • nova-clone

      Public
      Clone calling algorithm and QC
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated May 10, 2026May 10, 2026

    • resolvi-reproducibility

      Public
      Reproducibility notebooks for resolVI manuscript
      Python
      •2•13•0•0•Updated Apr 17, 2026Apr 17, 2026

    • cytovi-reproducibility

      Public
      Reproducibility repository for the CytoVI manuscript
      Jupyter Notebook
      •2•7•0•0•Updated Apr 1, 2026Apr 1, 2026

    • Hotspot

      Public
      Python
      •
      MIT License
      •19•167•22•0•Updated Mar 20, 2026Mar 20, 2026

    • scvi-hub-models

      Public
      Reproducibility workflows for pre-trained scvi-tools models on Hugging Face
      Jupyter Notebook
      •
      MIT License
      •1•2•1•1•Updated Mar 1, 2026Mar 1, 2026

    • velovi

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•45•8•2•Updated Jan 12, 2026Jan 12, 2026

    • Thymus_CITE-seq

      Public
      Jupyter Notebook
      •
      MIT License
      •0•5•0•0•Updated Dec 27, 2025Dec 27, 2025

    • CellRangerIDE

      Public
      Python
      •0•1•0•0•Updated Nov 30, 2025Nov 30, 2025

    • Compass

      Public
      In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •33•127•53•2•Updated Oct 31, 2025Oct 31, 2025

    • scVI-data

      Public
      datasets for scVI
      2•4•0•0•Updated May 21, 2025May 21, 2025

    • cytovi-reference-implementation

      Public
      Python
      •
      MIT License
      •1•4•1•1•Updated Apr 23, 2025Apr 23, 2025

    • scvi-hub-reproducibility

      Public
      Reproducibility of results/figures from scvi-hub paper
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•15•0•0•Updated Apr 16, 2025Apr 16, 2025
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