Repositories list

• scarches

  Public
  Reference mapping for single-cell genomics

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •63•0•0•0•Updated Aug 4, 2025Aug 4, 2025

• cell-annotator

  Public
  Automatically annotate cell types, consistently across samples.

  annotationgenomicsscrna-seq+ 2single-cellllm

  Python

  •

  MIT License

  •1•15•1•1•Updated Aug 4, 2025Aug 4, 2025

• task_predict_modality

  Public
  Predicting the profiles of one modality (e.g. protein abundance) from another (e.g. mRNA expression).

  Python

  •

  MIT License

  •1•0•0•0•Updated Jul 31, 2025Jul 31, 2025

• cellmapper

  Public
  k-NN-based mapping of cells across representations to transfer labels, embeddings, and expression values.

  genomicsscrna-seqdata-integration+ 4representation-learningsingle-cellk-nnspatial-biology

  Python

  •

  MIT License

  •0•6•3•2•Updated Jul 30, 2025Jul 30, 2025

• task_denoising

  Public
  Removing noise in sparse single-cell RNA-sequencing count data

  Python

  •

  MIT License

  •3•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

  •3•0•0•0•Updated Jul 29, 2025Jul 29, 2025

• slurm_sweep

  Public
  Hyperparameter sweeps on SLURM clusters

  Python

  •

  MIT License

  •0•3•1•1•Updated Jul 28, 2025Jul 28, 2025

• iNeuron_patterning

  Public
  Jupyter Notebook

  •1•5•0•0•Updated Jul 28, 2025Jul 28, 2025

• 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

  •35•0•0•0•Updated Jul 4, 2025Jul 4, 2025

• morphodynamics_human_brain_organoid

  Public
  Jupyter Notebook

  •

  MIT License

  •2•3•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

  •0•0•0•0•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

  •56•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

• scib-metrics

  Public
  Accelerated, Python-only, single-cell integration benchmarking metrics

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •16•0•0•0•Updated Apr 10, 2025Apr 10, 2025

• simple_slurm

  Public
  A simple Python wrapper for Slurm with flexibility in mind.

  Python

  •

  GNU Affero General Public License v3.0

  •25•0•0•0•Updated Apr 8, 2025Apr 8, 2025

• HNOCA-tools

  Public
  Toolbox of the Human Neural Organoid Cell Atlas

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Apr 1, 2025Apr 1, 2025

• scRNAseq_analysis_vignette

  Public
  Tutorial for scRNA-seq data analysis beginners using R

  bioinformaticstutorialsingle-cell-rna-seq+ 1single-cell-analysis

  67•210•2•0•Updated Mar 5, 2025Mar 5, 2025

• scRNAseq_analysis_python_vignette

  Public
  Tutorial of scRNA-seq data analysis with Python

  HTML

  •0•5•0•0•Updated Mar 5, 2025Mar 5, 2025

• spatialdata-plot

  Public
  Static plotting for spatialdata

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •17•0•0•0•Updated Feb 21, 2025Feb 21, 2025

• amex_merfish_spaceolotl

  Public
  Python

  •0•0•0•0•Updated Jan 6, 2025Jan 6, 2025

• 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 Nov 10, 2024Nov 10, 2024

• RNAseq_tutorial

  Public
  8•29•0•0•Updated Oct 16, 2024Oct 16, 2024

• moscot

  Public
  Multi-omic single-cell optimal transport tools

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •10•0•0•0•Updated Jul 26, 2024Jul 26, 2024

• Tangram

  Public
  Spatial alignment of single cell transcriptomic data.

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •57•0•0•0•Updated Jul 3, 2024Jul 3, 2024

• scMultiome_analysis_vignette

  Public
  Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis

  tutorialsingle-cell-rna-seqsingle-cell-analysis+ 3single-cell-atac-seqsingle-cell-multiomicsbioinformatics

  15•63•6•0•Updated Apr 22, 2024Apr 22, 2024

• Pando

  Public
  Multiome GRN inference.

  transcriptomicssingle-cellepigenomics

  R

  •

  MIT License

  •23•125•24•3•Updated Apr 19, 2024Apr 19, 2024

• organoid_epigenomics

  Public
  R

  •0•8•1•0•Updated Apr 12, 2024Apr 12, 2024

• simspec

  Public
  Calculation of Reference/Cluster Similarity Spectrum (RSS/CSS)

  batch-correctionsingle-cell-analysis

  R

  •3•32•5•0•Updated Mar 6, 2024Mar 6, 2024

• VoxHunt

  Public
  VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps

  single-cellorganoids

  HTML

  •

  MIT License

  •6•46•2•0•Updated Mar 1, 2024Mar 1, 2024

• latent-lego

  Public
  Latent spaces for single cells

  Jupyter Notebook

  •

  MIT License

  •0•21•0•0•Updated Oct 31, 2023Oct 31, 2023