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    69 repositories

    • pycea

      Public
      scverse lineage tracing analysis toolkit
      bioinformaticsscanpylineage-tracing
      bioinformaticsscanpylineage-tracingtreedatascverse
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•4•0•1•Updated Mar 24, 2026Mar 24, 2026

    • scib-metrics

      Public
      Accelerated, Python-only, single-cell integration benchmarking metrics
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •20•89•7•3•Updated Mar 24, 2026Mar 24, 2026

    • popV

      Public
      Python
      •
      MIT License
      •20•92•3•2•Updated Mar 23, 2026Mar 23, 2026

    • destvi_utils

      Public
      Utilities for downstream analysis of destVI
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•1•1•Updated Mar 23, 2026Mar 23, 2026

    • treedata

      Public
      anndata with trees
      data-sciencebioinformaticsscanpy
      data-sciencebioinformaticsscanpyanndatalineage-tracingscverse
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•8•0•1•Updated Mar 23, 2026Mar 23, 2026

    • Hotspot

      Public
      Python
      •
      MIT License
      •17•145•20•0•Updated Mar 20, 2026Mar 20, 2026

    • mrvi_archive

      Public
      Multi-resolution Variational Inference
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•23•2•1•Updated Mar 16, 2026Mar 16, 2026

    • scvi-hub-models

      Public
      Reproducibility workflows for pre-trained scvi-tools models on Hugging Face
      Jupyter Notebook
      •
      MIT License
      •1•1•1•1•Updated Mar 1, 2026Mar 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
      •29•99•23•13•Updated Feb 5, 2026Feb 5, 2026

    • cytovi-reproducibility

      Public
      Reproducibility repository for the CytoVI manuscript
      Jupyter Notebook
      •2•1•0•0•Updated Jan 22, 2026Jan 22, 2026

    • velovi

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•41•8•2•Updated Jan 12, 2026Jan 12, 2026

    • csde

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•7•0•0•Updated Jan 10, 2026Jan 10, 2026

    • Thymus_CITE-seq

      Public
      Jupyter Notebook
      •
      MIT License
      •0•4•0•0•Updated Dec 27, 2025Dec 27, 2025

    • Harreman

      Public
      Harreman infers metabolic exchanges in tissues using spatial transcriptomics.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•7•0•0•Updated Dec 9, 2025Dec 9, 2025

    • visionpy

      Public
      Functional interpretation of single cell similarity maps
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •4•5•0•3•Updated Dec 2, 2025Dec 2, 2025

    • CellRangerIDE

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

    • Harreman-reproducibility

      Public
      Reproducibility repository for the Harreman manuscript.
      Jupyter Notebook
      •0•0•0•0•Updated Nov 18, 2025Nov 18, 2025

    • yoseflab.github.io

      Public
      JavaScript
      •
      MIT License
      •9•3•0•0•Updated Nov 13, 2025Nov 13, 2025

    • Compass

      Public
      In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •33•123•52•2•Updated Oct 31, 2025Oct 31, 2025

    • VIVS

      Public
      Calibrated Identification of Feature Dependencies in Single-cell Multiomics
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•5•0•0•Updated Jul 8, 2025Jul 8, 2025

    • scVI-data

      Public
      datasets for scVI
      2•3•0•0•Updated May 21, 2025May 21, 2025

    • resolvi-reproducibility

      Public
      Reproducibility notebooks for resolVI manuscript
      Jupyter Notebook
      •0•6•0•0•Updated May 8, 2025May 8, 2025

    • cytovi-reference-implementation

      Public
      Python
      •
      MIT License
      •1•0•0•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•12•0•0•Updated Apr 16, 2025Apr 16, 2025

    • scone

      Public
      R
      •11•55•31•1•Updated Feb 19, 2025Feb 19, 2025

    • mrvi-reproducibility

      Public
      Nextflow pipeline for MrVI pipelines
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•9•1•Updated Feb 10, 2025Feb 10, 2025

    • mrvi

      Public archive
      Multi-resolution Variational Inference
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•7•4•0•Updated Oct 9, 2024Oct 9, 2024

    • SymSim

      Public
      HTML
      •7•27•1•0•Updated Sep 26, 2024Sep 26, 2024

    • scvi-tools-docker

      Public archive
      Docker images for scvi-tools
      Dockerfile
      •
      MIT License
      •1•2•0•0•Updated Jul 12, 2024Jul 12, 2024

    • popv-reproducibility

      Public
      Reproducibility for popV
      Jupyter Notebook
      •3•2•0•0•Updated Jun 28, 2024Jun 28, 2024