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@openproblems-bio Open Problems in Single-Cell Analysis

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    33 repositories

    • task_grn_inference

      Public
      Jupyter Notebook
      •1•3•0•0•Updated Nov 14, 2024Nov 14, 2024

    • website

      Public
      Website hosted at https://openproblems.bio
      TeX
      •
      Creative Commons Attribution 4.0 International
      •8•3•32•17•Updated Nov 13, 2024Nov 13, 2024

    • openproblems

      Public
      Formalizing and benchmarking open problems in single-cell genomics
      Shell
      •
      MIT License
      •80•320•7•2•Updated Nov 13, 2024Nov 13, 2024

    • task_ist_preprocessing

      Public
      Shell
      •
      MIT License
      •0•2•0•1•Updated Nov 13, 2024Nov 13, 2024

    • task_perturbation_prediction

      Public
      A benchmark on predicting how small molecules change gene expression in different cell types.
      Python
      •
      MIT License
      •1•3•2•2•Updated Nov 11, 2024Nov 11, 2024

    • task_batch_integration

      Public
      Python
      •
      MIT License
      •1•0•1•0•Updated Nov 9, 2024Nov 9, 2024

    • task_spatial_decomposition

      Public
      Python
      •0•0•1•0•Updated Nov 6, 2024Nov 6, 2024

    • task_spatially_variable_genes

      Public
      A benchmark on detecting genes whose expression levels vary across spatial regions.
      Python
      •
      MIT License
      •0•0•1•0•Updated Nov 5, 2024Nov 5, 2024

    • task_dimensionality_reduction

      Public
      Python
      •
      MIT License
      •1•0•4•0•Updated Nov 5, 2024Nov 5, 2024

    • task_cyto_batch_integration

      Public
      Shell
      •
      MIT License
      •1•1•2•0•Updated Nov 5, 2024Nov 5, 2024

    • 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
      •1•1•0•0•Updated Nov 5, 2024Nov 5, 2024

    • common_resources

      Public
      This repo contains common resources that can be used for OpenProblems v2 tasks.
      TeX
      •
      MIT License
      •1•0•1•0•Updated Oct 31, 2024Oct 31, 2024

    • task_spatial_simulators

      Public
      Benchmarking spatial simulators
      R
      •
      MIT License
      •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • core

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • task_denoising

      Public
      Removing noise in sparse single-cell RNA-sequencing count data
      Python
      •
      MIT License
      •0•0•1•0•Updated Oct 2, 2024Oct 2, 2024

    • task_cell_cell_communication

      Public
      Predicting cell-cell interactions between source cell types and target cell types.
      Shell
      •
      MIT License
      •1•0•0•0•Updated Sep 26, 2024Sep 26, 2024

    • task_predict_modality

      Public
      Predicting the profiles of one modality (e.g. protein abundance) from another (e.g. mRNA expression).
      R
      •
      MIT License
      •0•0•0•3•Updated Sep 20, 2024Sep 20, 2024

    • nbt2023-manuscript

      Public
      R
      •0•1•0•0•Updated Sep 16, 2024Sep 16, 2024

    • test

      Public
      Shell
      •
      MIT License
      •0•0•0•0•Updated Sep 11, 2024Sep 11, 2024

    • task_label_projection

      Public
      Automated cell type annotation from rich, labeled reference data
      Python
      •
      MIT License
      •0•0•1•0•Updated Sep 7, 2024Sep 7, 2024

    • openproblems-v2

      Public
      Formalizing and benchmarking open problems in single-cell genomics
      benchmarkingsingle-cellnextflowviash
      Python
      •
      MIT License
      •19•56•31•5•Updated Sep 4, 2024Sep 4, 2024

    • base_images

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

    • 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•10•1•0•Updated Nov 23, 2023Nov 23, 2023

    • neurips2022_multimodal_topmethods

      Public
      Shell
      •0•2•0•0•Updated Jun 6, 2023Jun 6, 2023

    • website-experimental

      Public archive
      Experimental website to try out new content for the main website
      TeX
      •0•3•0•4•Updated Mar 10, 2023Mar 10, 2023

    • nf-openproblems

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Feb 13, 2023Feb 13, 2023

    • NeurIPS21_comp_paper_reproducibility

      Public
      Scripts and notebooks to reproduce the analysis of the NeurIPS 2021 competition paper submitted to PMLR
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 28, 2022Nov 28, 2022

    • neurips-2022-notebooks

      Public
      Notebooks used to process the data for the Open Problems competition at NeurIPS 2022
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 17, 2022Oct 17, 2022

    • neurips_2022_saturn_notebooks

      Public
      Notebooks for exploring data associated with the Open Problems competition on Kaggle, presented at NeurIPS 2022
      Jupyter Notebook
      •
      MIT License
      •5•5•0•0•Updated Sep 24, 2022Sep 24, 2022