Repositories list

• archmap

  Public
  JavaScript

  •

  MIT License

  •0•4•3•0•Updated Jan 28, 2025Jan 28, 2025

• single-cell-best-practices

  Public
  https://www.sc-best-practices.org

  tutorialrna-seqbook+ 1single-cell

  Jupyter Notebook

  •

  Other

  •198•826•69•4•Updated Jan 28, 2025Jan 28, 2025

• archmap_data

  Public
  Python

  •0•1•1•1•Updated Jan 28, 2025Jan 28, 2025

• moscot

  Public
  Multi-omic single-cell optimal transport tools

  single-celloptimal-transport

  Python

  •

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

  •9•127•37•4•Updated Jan 28, 2025Jan 28, 2025

• anndata2ri

  Public
  Convert between AnnData and SingleCellExperiment

  jupyterbioconductorsingle-cell+ 2rpy2scanpy

  Python

  •

  GNU General Public License v3.0

  •16•130•13•0•Updated Jan 27, 2025Jan 27, 2025

• scanpydoc

  Public
  Collection of Sphinx extensions similar to (but more flexible than) numpydoc

  Python

  •

  GNU General Public License v3.0

  •6•12•2•0•Updated Jan 27, 2025Jan 27, 2025

• ehrdata

  Public
  A datastructure for EHR data

  Python

  •

  Apache License 2.0

  •1•5•20•1•Updated Jan 27, 2025Jan 27, 2025

• ehrapy

  Public
  Electronic Health Record Analysis with Python.

  ehrelectronic-health-recordscverse+ 1electronic-medical-record

  Python

  •

  Apache License 2.0

  •22•259•42•1•Updated Jan 27, 2025Jan 27, 2025

• multigrate

  Public
  Multigrate: multiomic data integration for single-cell genomics

  Python

  •

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

  •6•17•4•2•Updated Jan 27, 2025Jan 27, 2025

• DRVI

  Public
  Unsupervised Deep Disentangled Representation of Single-Cell Omics

  pythonbioinformaticsintegration+ 4transcriptomicssingle-celldisentanglementanndata

  Python

  •

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

  •3•35•2•1•Updated Jan 27, 2025Jan 27, 2025

• gh-dashboard

  Public
  A dashboard of everything in the theislab GitHub repository

  HTML

  •0•3•0•0•Updated Jan 27, 2025Jan 27, 2025

• pertpy-reproducibility

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •1•1•0•3•Updated Jan 26, 2025Jan 26, 2025

• chemCPA

  Public
  Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

  genomicsdrug-discoverytransfer-learning+ 3single-cellperturbationdisentanglement

  Jupyter Notebook

  •

  MIT License

  •24•105•13•0•Updated Jan 24, 2025Jan 24, 2025

• scib-pipeline

  Public
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.

  Python

  •

  MIT License

  •27•68•12•4•Updated Jan 23, 2025Jan 23, 2025

• moscot_notebooks

  Public
  Analysis notebooks using the moscot package

  Jupyter Notebook

  •

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

  •4•8•3•2•Updated Jan 22, 2025Jan 22, 2025

• spatialdata-db

  Public
  Jupyter Notebook

  •

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

  •0•1•25•0•Updated Jan 22, 2025Jan 22, 2025

• single-cell-transformer-papers

  Public
  HTML

  •

  Other

  •38•289•41•1•Updated Jan 21, 2025Jan 21, 2025

• regvelo

  Public
  inferring regulatory cellular dynamics

  generative-modelrna-velocity-estimationperturbation-analysis+ 2grn-inferencesingle-cell-dynamics

  Python

  •

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

  •1•27•1•0•Updated Jan 21, 2025Jan 21, 2025

• inVAE_reproducibility

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

• graphcompass

  Public
  GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems

  Jupyter Notebook

  •

  MIT License

  •0•34•1•0•Updated Jan 15, 2025Jan 15, 2025

• scib

  Public
  Benchmarking analysis of data integration tools

  Python

  •

  MIT License

  •64•325•34•6•Updated Jan 14, 2025Jan 14, 2025

• scarches

  Public
  Reference mapping for single-cell genomics

  deep-learningscrna-seqdata-integration+ 7single-cellrna-seq-analysissingle-cell-genomicsbatch-correctionmultimodal-deep-learningmultiomicshuman-cell-atlas

  Jupyter Notebook

  •

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

  •52•348•48•7•Updated Jan 11, 2025Jan 11, 2025

• IMPA

  Public
  Jupyter Notebook

  •1•10•0•0•Updated Jan 10, 2025Jan 10, 2025

• regvelo_reproducibility

  Public
  Jupyter Notebook

  •

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

  •0•4•0•0•Updated Jan 7, 2025Jan 7, 2025

• nicheformer

  Public
  Repository for Nicheformer: a foundation model for single-cell and spatial omics

  Jupyter Notebook

  •

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

  •3•78•16•0•Updated Jan 6, 2025Jan 6, 2025

• prophet

  Public
  Python

  •

  MIT License

  •2•27•3•0•Updated Dec 22, 2024Dec 22, 2024

• moscot-framework_reproducibility

  Public
  Data analysis for the moscot-framework project

  Jupyter Notebook

  •0•6•1•0•Updated Dec 20, 2024Dec 20, 2024

• neural_organoid_atlas

  Public
  Reproducibility repository for the Human Neural Organoid Atlas publication

  Jupyter Notebook

  •4•26•2•1•Updated Dec 16, 2024Dec 16, 2024

• cellrank

  Public
  CellRank: dynamics from multi-view single-cell data

  data-sciencemachine-learningbioinformatics+ 10geneticstrajectory-generationmarkov-chainsmanifold-learningsingle-cell-genomicssingle-cell-rna-seqcell-fate-transitions+ 3

  Python

  •

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

  •47•360•18•0•Updated Dec 14, 2024Dec 14, 2024

• zellkonverter

  Public
  Conversion between scRNA-seq objects

  rconversionscrna-seq+ 1bioconductor

  R

  •

  Other

  •28•157•12•1•Updated Dec 10, 2024Dec 10, 2024