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    52 repositories

    • scMultiome_analysis_vignette

      Public
      Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis
      bioinformaticstutorialsingle-cell-rna-seq
      bioinformaticstutorialsingle-cell-rna-seqsingle-cell-analysissingle-cell-atac-seqsingle-cell-multiomics
      17•78•6•0•Updated Apr 16, 2026Apr 16, 2026

    • scMultiome_analysis_python_vignette

      Public
      Tutorial of scMultiome (RNA-ATAC) data analysis with Python
      HTML
      •0•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • scBulkDE

      Public
      Performing differential testing on pseudobulked single-cell data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 15, 2026Apr 15, 2026

    • posterior_multiome

      Public
      Code repo for the manuscript: "Multi-omic human neural organoid cell atlas of the posterior brain"
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Apr 14, 2026Apr 14, 2026

    • pysimspec

      Public
      Python implementation of simspec (for RSS/CSS)
      Python
      •
      MIT License
      •0•1•0•0•Updated Apr 14, 2026Apr 14, 2026

    • cellmapper

      Public
      k-NN-based mapping of cells across representations to transfer labels, embeddings, and expression values.
      genomicsscrna-seqdata-integration
      genomicsscrna-seqdata-integrationrepresentation-learningsingle-cellk-nnspatial-biology
      Python
      •
      MIT License
      •4•13•4•1•Updated Apr 13, 2026Apr 13, 2026

    • slurm_sweep

      Public
      Hyperparameter sweeps on SLURM clusters
      Python
      •
      MIT License
      •2•5•1•2•Updated Apr 13, 2026Apr 13, 2026

    • scembed

      Public
      Run embedding comparisons for single-cell data
      bioinformaticsscrna-seqdata-integration
      bioinformaticsscrna-seqdata-integrationspatial-genomics
      Python
      •
      MIT License
      •1•5•0•4•Updated Apr 13, 2026Apr 13, 2026

    • cell-annotator

      Public
      Automatically annotate cell types, consistently across samples.
      annotationgenomicsscrna-seq
      annotationgenomicsscrna-seqsingle-cellllm
      Python
      •
      MIT License
      •2•20•3•3•Updated Apr 13, 2026Apr 13, 2026

    • Pando

      Public
      Multiome GRN inference.
      transcriptomicssingle-cellepigenomics
      transcriptomicssingle-cellepigenomics
      R
      •
      MIT License
      •24•135•26•3•Updated Apr 10, 2026Apr 10, 2026

    • scvi-tools-public

      Public
      Deep probabilistic analysis of single-cell and spatial omics data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •446•0•0•0•Updated Apr 1, 2026Apr 1, 2026

    • simspec

      Public
      Calculation of Reference/Cluster Similarity Spectrum (RSS/CSS)
      batch-correctionsingle-cell-analysis
      batch-correctionsingle-cell-analysis
      R
      •3•40•4•0•Updated Mar 31, 2026Mar 31, 2026

    • hydra-sweeper-explicit

      Public
      Sweeper plugin for explicit multirun configs in hydra
      Python
      •
      MIT License
      •0•1•0•0•Updated Mar 31, 2026Mar 31, 2026

    • squidpy

      Public
      Spatial Single Cell Analysis in Python
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •113•0•0•0•Updated Mar 23, 2026Mar 23, 2026

    • scvi-tutorials

      Public
      Notebooks used in scvi-tools tutorials
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •32•0•0•0•Updated Mar 18, 2026Mar 18, 2026

    • sopa

      Public
      Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •48•0•0•0•Updated Feb 26, 2026Feb 26, 2026

    • analysis_template

      Public template
      Simple template repo for single-cell/spatial analysis
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Feb 19, 2026Feb 19, 2026

    • pygpcca_speedup_analysis

      Public
      Experiment with gradient-based optimization for pyGPCCA
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

    • transcriptomic_clustering

      Public
      Allen Institute Transcriptomic Clustering Pipeline
      Python
      •
      Other
      •4•0•0•0•Updated Feb 9, 2026Feb 9, 2026

    • novae

      Public
      Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many other features.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •12•2•0•0•Updated Jan 15, 2026Jan 15, 2026

    • organoid_patterning_screen

      Public
      This repository contains the code to reproduce the analysis in the manuscript "Systematic neural organoid scRNA-seq screens measure morphogen response" (Sanchís…
      Jupyter Notebook
      •0•5•0•0•Updated Dec 15, 2025Dec 15, 2025

    • iNeuron_patterning

      Public
      Jupyter Notebook
      •2•7•0•0•Updated Oct 22, 2025Oct 22, 2025

    • scarches

      Public
      Reference mapping for single-cell genomics
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •70•0•0•0•Updated Aug 15, 2025Aug 15, 2025

    • task_predict_modality

      Public
      Predicting the profiles of one modality (e.g. protein abundance) from another (e.g. mRNA expression).
      Python
      •
      MIT License
      •2•0•0•0•Updated Aug 13, 2025Aug 13, 2025

    • task_denoising

      Public
      Removing noise in sparse single-cell RNA-sequencing count data
      Python
      •
      MIT License
      •5•0•0•0•Updated Jul 29, 2025Jul 29, 2025

    • task_label_projection

      Public
      Automated cell type annotation from rich, labeled reference data
      Python
      •
      MIT License
      •6•0•0•0•Updated Jul 29, 2025Jul 29, 2025

    • morphodynamics_human_brain_organoid

      Public
      Jupyter Notebook
      •
      MIT License
      •3•10•0•0•Updated Jun 18, 2025Jun 18, 2025

    • atac_mapper

      Public
      Map query scATAC-seq data to a single-cell chromatin accessibility atlas
      Python
      •
      MIT License
      •1•0•0•1•Updated Jun 17, 2025Jun 17, 2025

    • ecosystem-packages

      Public
      Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •74•0•0•0•Updated May 2, 2025May 2, 2025

    • BVO_fate_and_state_transitions

      Public
      R
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Apr 11, 2025Apr 11, 2025
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