https://github.com/berenslab/ne_spectrum_scrnaseq

Science Score: 49.0%

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Last synced: 6 months ago · JSON representation

Repository

Basic Info

Host: GitHub
Owner: berenslab
License: mit
Language: Jupyter Notebook
Default Branch: main
Size: 47.8 MB

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Stars: 2
Watchers: 2
Forks: 1
Open Issues: 1
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Created almost 2 years ago · Last pushed 10 months ago

Metadata Files

Readme License

README.md

Neighbor embedding spectrum for single-cell data

This repository contains scripts and notebooks to reproduce the experiments in Visualizing single-cell data with the neighbor embedding spectrum (bioarxiv)

It depends on the ne-spectrum package, which computes neighbor embedding spectra.

NE spectrum on Kanton et al. data

Neighbor embedding spectrum on developmental human brain organoid data from Kanton et al. 2019.

Neighbor embedding spectrum on Kanton et al. data animated

Higher attraction improves the global structure as measured by Spearman distance correlation. Higher repulsion improves local structure as measured by kNN recall.

Global and local metric along the spectrum

Installation

Create and activate the conda environment conda env create -f environment.yml conda activate ne_spectrum_scRNAseq

Install the utilities for this repository python setup.py install

Usage

To reproduce the data for the figures in the main paper, run python scripts/compute_embds.py --spectrum_via tsne python scripts/compute_metrics.py --spectrum_via tsne

To reproduce the data for the figures in the supplementary, run python scripts/compute_embds.py --spectrum_via cne python scripts/compute_metrics.py --spectrum_via cne

Then run the notebooks in notebooks/ to generate the figures and the videos.

Owner

Name: Berens Lab @ University of Tübingen
Login: berenslab
Kind: organization
Email: philipp.berens@uni-tuebingen.de
Location: Tübingen, Germany

Website: https://hertie.ai/data-science
Repositories: 60
Profile: https://github.com/berenslab

Department of Data Science at the Hertie Institute for AI in Brain Health, University of Tübingen

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