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@openproblems-bio Open Problems in Single-Cell Analysis

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    39 repositories

    • task_ist_preprocessing

      Public
      Python
      •
      MIT License
      •4•9•9•7•Updated Feb 27, 2026Feb 27, 2026

    • task_cyto_batch_integration

      Public
      R
      •
      MIT License
      •1•2•5•1•Updated Feb 11, 2026Feb 11, 2026

    • task_grn_inference

      Public
      Jupyter Notebook
      •
      MIT License
      •5•17•3•2•Updated Jan 30, 2026Jan 30, 2026

    • logos

      Public
      The Open Problems logo in different formats
      logos
      Shell
      •
      Creative Commons Attribution Share Alike 4.0 International
      •0•0•0•0•Updated Nov 28, 2025Nov 28, 2025

    • openproblems

      Public
      Formalizing and benchmarking open problems in single-cell genomics
      TeX
      •
      MIT License
      •88•420•13•0•Updated Nov 26, 2025Nov 26, 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•4•1•2•Updated Nov 26, 2025Nov 26, 2025

    • core

      Public
      R
      •
      MIT License
      •0•0•0•2•Updated Nov 21, 2025Nov 21, 2025

    • task_batch_integration

      Public
      Python
      •
      MIT License
      •16•12•11•22•Updated Nov 7, 2025Nov 7, 2025

    • task_denoising

      Public
      Removing noise in sparse single-cell RNA-sequencing count data
      Python
      •
      MIT License
      •5•3•3•2•Updated Nov 6, 2025Nov 6, 2025

    • task_label_projection

      Public
      Automated cell type annotation from rich, labeled reference data
      Python
      •
      MIT License
      •4•5•3•4•Updated Oct 19, 2025Oct 19, 2025

    • task_dimensionality_reduction

      Public
      Python
      •
      MIT License
      •3•1•5•2•Updated Sep 29, 2025Sep 29, 2025

    • common_resources

      Public
      Common resources for various benchmarks.
      Nextflow
      •
      MIT License
      •1•0•2•0•Updated Sep 29, 2025Sep 29, 2025

    • .github

      Public
      MIT License
      •0•0•0•0•Updated Sep 15, 2025Sep 15, 2025

    • datasets

      Public
      Shell
      •
      MIT License
      •0•0•1•1•Updated Sep 10, 2025Sep 10, 2025

    • task_template

      Public template
      This repo is a template to create a new task that has the correct files and structure needed to start a new task.
      Shell
      •
      MIT License
      •2•2•1•0•Updated Sep 2, 2025Sep 2, 2025

    • task_spatial_simulators

      Public
      Benchmarking spatial simulators
      R
      •
      MIT License
      •1•0•1•1•Updated Aug 27, 2025Aug 27, 2025

    • task_differential_expression

      Public
      Shell
      •
      MIT License
      •0•0•0•0•Updated Aug 19, 2025Aug 19, 2025

    • task_perturbation_prediction

      Public
      A benchmark on predicting how small molecules change gene expression in different cell types.
      Python
      •
      MIT License
      •3•16•5•4•Updated Jul 4, 2025Jul 4, 2025

    • nbt2025-manuscript

      Public
      R
      •0•2•0•0•Updated Jun 26, 2025Jun 26, 2025

    • docs

      Public
      TeX
      •3•1•10•2•Updated Jun 18, 2025Jun 18, 2025

    • task_spatial_decomposition

      Public
      Python
      •0•0•1•0•Updated Jun 11, 2025Jun 11, 2025

    • task_cell_cell_communication

      Public
      Predicting cell-cell interactions between source cell types and target cell types.
      Shell
      •
      MIT License
      •2•1•0•1•Updated Jun 11, 2025Jun 11, 2025

    • task_spatially_variable_genes

      Public
      A benchmark on detecting genes whose expression levels vary across spatial regions.
      Python
      •
      MIT License
      •1•2•1•5•Updated Jun 11, 2025Jun 11, 2025

    • openproblems-v2

      Public
      Formalizing and benchmarking open problems in single-cell genomics
      benchmarkingnextflowsingle-cellviash
      Python
      •
      MIT License
      •20•57•31•6•Updated Jun 11, 2025Jun 11, 2025

    • task_workshop_example

      Public
      An example of a new task to use in workshops. NOTE THIS REPOSITORY IS INCOMPLETE. See INSTRUCTIONS.md for instructions on how to use it.
      Python
      •
      MIT License
      •0•0•0•1•Updated Jun 11, 2025Jun 11, 2025

    • website

      Public
      Legacy website
      TeX
      •
      Creative Commons Attribution 4.0 International
      •8•5•33•14•Updated Jun 11, 2025Jun 11, 2025

    • task_foundation_models

      Public
      Shell
      •
      MIT License
      •0•0•2•1•Updated Jun 3, 2025Jun 3, 2025

    • base_images

      Public archive
      MIT License
      •0•0•2•0•Updated Sep 4, 2024Sep 4, 2024

    • explore-datasets

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jun 14, 2024Jun 14, 2024

    • neurips-2023-scripts

      Public
      Scripts associated with the 2023 Open Problems competition
      Jupyter Notebook
      •
      MIT License
      •0•11•1•0•Updated Nov 23, 2023Nov 23, 2023