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    68 repositories

    • Thymus_CITE-seq

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

    • scib-metrics

      Public
      Accelerated, Python-only, single-cell integration benchmarking metrics
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •20•80•7•2•Updated Dec 23, 2025Dec 23, 2025

    • destvi_utils

      Public
      Utilities for downstream analysis of destVI
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•1•1•Updated Dec 22, 2025Dec 22, 2025

    • treedata

      Public
      anndata with trees
      data-sciencebioinformaticsscanpyanndatalineage-tracingscverse
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•7•0•2•Updated Dec 22, 2025Dec 22, 2025

    • velovi

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•40•8•2•Updated Dec 22, 2025Dec 22, 2025

    • popV

      Public
      Python
      •
      MIT License
      •19•85•2•3•Updated Dec 22, 2025Dec 22, 2025

    • pycea

      Public
      scverse lineage tracing analysis toolkit
      bioinformaticsscanpylineage-tracingtreedatascverse
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•4•0•1•Updated Dec 12, 2025Dec 12, 2025

    • Harreman

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

    • mrvi_archive

      Public
      Multi-resolution Variational Inference
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•22•2•1•Updated Dec 8, 2025Dec 8, 2025

    • Cassiopeia

      Public
      A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
      computational-biologycrispr-cas9single-cell-rna-seqlineage-tracingsingle-cell-lineage-tracingcomputational-phylogenetics
      Python
      •
      MIT License
      •28•97•23•13•Updated Dec 8, 2025Dec 8, 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
      •32•119•52•2•Updated Oct 31, 2025Oct 31, 2025

    • cytovi-reproducibility

      Public
      Reproducibility repository for the CytoVI manuscript
      Jupyter Notebook
      •1•1•0•0•Updated Sep 12, 2025Sep 12, 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

    • Hotspot

      Public
      Python
      •
      MIT License
      •16•140•22•0•Updated Apr 19, 2025Apr 19, 2025

    • scvi-hub-reproducibility

      Public
      Reproducibility of results/figures from scvi-hub paper
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•11•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

    • scvi-hub-models

      Public
      Reproducibility workflows for pre-trained scvi-tools models on Hugging Face
      Jupyter Notebook
      •
      MIT License
      •1•1•1•1•Updated Dec 13, 2024Dec 13, 2024

    • mrvi

      Public archive
      Multi-resolution Variational Inference
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•6•4•0•Updated Oct 9, 2024Oct 9, 2024

    • SymSim

      Public
      HTML
      •7•26•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

    • VISION

      Public
      Signature Analysis and Visualization for Single-Cell RNA-seq
      R
      •
      MIT License
      •33•174•32•4•Updated Jun 10, 2024Jun 10, 2024