Repositories list

• task_spatial_segmentation

  Public

  openproblems-bio/task_spatial_segmentation’s past year of commit activity
  Python

  •

  MIT License

  •33 forks•55 stars•77 issues•44 pull requests•Updated May 18, 2026May 18, 2026

• task_cyto_batch_integration

  Public

  openproblems-bio/task_cyto_batch_integration’s past year of commit activity
  R

  •

  MIT License

  •11 fork•22 stars•55 issues•00 pull requests•Updated May 14, 2026May 14, 2026

• task_ist_preprocessing

  Public

  openproblems-bio/task_ist_preprocessing’s past year of commit activity
  Python

  •

  MIT License

  •44 forks•99 stars•99 issues•1010 pull requests•Updated May 13, 2026May 13, 2026

• task_grn_inference

  Public

  openproblems-bio/task_grn_inference’s past year of commit activity
  Python

  •

  MIT License

  •55 forks•1717 stars•22 issues•22 pull requests•Updated May 8, 2026May 8, 2026

• openproblems

  Public
  Formalizing and benchmarking open problems in single-cell genomics

  TeX

  •

  MIT License

  •8888 forks•428428 stars•1313 issues•00 pull requests•Updated May 7, 2026May 7, 2026

• datasets

  Public

  openproblems-bio/datasets’s past year of commit activity
  Shell

  •

  MIT License

  •11 fork•00 stars•11 issue•11 pull request•Updated May 7, 2026May 7, 2026

• task_dimensionality_reduction

  Public
  Python

  •

  MIT License

  •33 forks•11 star•55 issues•22 pull requests•Updated Apr 30, 2026Apr 30, 2026

• common_resources

  Public
  Common resources for various benchmarks.

  Nextflow

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  MIT License

  •11 fork•00 stars•22 issues•00 pull requests•Updated Apr 30, 2026Apr 30, 2026

• core

  Public

  openproblems-bio/core’s past year of commit activity
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• task_template

  Public template

  openproblems-bio/task_template’s past year of commit activity
  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

  •22 forks•22 stars•11 issue•00 pull requests•Updated Apr 21, 2026Apr 21, 2026

• logos

  Public
  The Open Problems logo in different formats

  logos

  logos

  Shell

  •

  Creative Commons Attribution Share Alike 4.0 International

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 28, 2025Nov 28, 2025

• task_predict_modality

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

  Python

  •

  MIT License

  •22 forks•44 stars•11 issue•22 pull requests•Updated Nov 26, 2025Nov 26, 2025

• task_batch_integration

  Public
  Python

  •

  MIT License

  •1717 forks•1313 stars•1212 issues•2323 pull requests•Updated Nov 7, 2025Nov 7, 2025

• task_denoising

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

  Python

  •

  MIT License

  •66 forks•44 stars•44 issues•22 pull requests•Updated Nov 6, 2025Nov 6, 2025

• task_label_projection

  Public
  Automated cell type annotation from rich, labeled reference data

  Python

  •

  MIT License

  •66 forks•55 stars•33 issues•66 pull requests•Updated Oct 19, 2025Oct 19, 2025

• .github

  Public
  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 15, 2025Sep 15, 2025

• task_spatial_simulators

  Public
  Benchmarking spatial simulators

  R

  •

  MIT License

  •11 fork•00 stars•11 issue•11 pull request•Updated Aug 27, 2025Aug 27, 2025

• task_differential_expression

  Public
  Shell

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•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

  •55 forks•1818 stars•55 issues•44 pull requests•Updated Jul 4, 2025Jul 4, 2025

• nbt2025-manuscript

  Public
  R

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jun 26, 2025Jun 26, 2025

• docs

  Public
  TeX

  •33 forks•11 star•1212 issues•22 pull requests•Updated Jun 18, 2025Jun 18, 2025

• task_spatial_decomposition

  Public
  Python

  •00 forks•00 stars•11 issue•00 pull requests•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

  •22 forks•11 star•00 issues•11 pull request•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

  •11 fork•22 stars•11 issue•55 pull requests•Updated Jun 11, 2025Jun 11, 2025

• openproblems-v2

  Public
  Formalizing and benchmarking open problems in single-cell genomics

  benchmarkingnextflowsingle-cell+ 1

  benchmarkingnextflowsingle-cellviash

  Python

  •

  MIT License

  •2020 forks•5656 stars•3131 issues•66 pull requests•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

  •00 forks•00 stars•00 issues•11 pull request•Updated Jun 11, 2025Jun 11, 2025

• website

  Public
  Legacy website

  TeX

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  Creative Commons Attribution 4.0 International

  •88 forks•55 stars•3333 issues•1414 pull requests•Updated Jun 11, 2025Jun 11, 2025

• task_foundation_models

  Public
  Shell

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  MIT License

  •00 forks•00 stars•22 issues•11 pull request•Updated Jun 3, 2025Jun 3, 2025

• base_images

  Public archive
  MIT License

  •00 forks•00 stars•22 issues•00 pull requests•Updated Sep 4, 2024Sep 4, 2024

• explore-datasets

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Jun 14, 2024Jun 14, 2024