Open Problems in Single-Cell Analysis

openproblems

Formalizing and benchmarking open problems in single-cell genomics

neurips2021_multimodal_topmethods

openproblems-v2

Formalizing and benchmarking open problems in single-cell genomics

neurips2021-notebooks

neurips2021_multimodal_viash

neurips-2023-scripts

Scripts associated with the 2023 Open Problems competition

neurips_2022_saturn_notebooks

Notebooks for exploring data associated with the Open Problems competition on Kaggle, presented at NeurIPS 2022

website

Website hosted at https://openproblems.bio

website-experimental

Experimental website to try out new content for the main website

neurips2022_multimodal_topmethods

datasets

nbt2023-manuscript

task_perturbation_prediction

A benchmark on predicting how small molecules change gene expression in different cell types.

base-images

NeurIPS21_comp_paper_reproducibility

Scripts and notebooks to reproduce the analysis of the NeurIPS 2021 competition paper submitted to PMLR

common-resources

This repo contains common resources that can be used for OpenProblems v2 tasks.

nf-openproblems

task-perturb-multiomics-grn

task-spatial-decomposition

task_cell_cell_communication

task_template

This repo is a template to create a new task that has the correct files and structure needed to start a new task.