csglab/GEDI_manuscript

This repository hosts R markdown notebooks reproducing the figures from the GEDI manuscript

GEDI manuscript

This repository hosts R markdown notebooks reproducing the figures from the GEDI manuscript.

Notebooks

• Fig 2: Analysis of sample-to-sample variability of PBMC data
• Fig. 2: Analysis of sample-to-sample variability of COVID-19 data
• Fig. 3: Transcriptomic vector field analysis of COVID-19 data
• Fig. 3: Comparison of mean transcriptomic vector fields
• Fig. 4: Comparison of cluster free differential expression methods
• Fig. 5: Inferring cell type signatures of PBMC data
• Fig. 5: Inferring TF activities of PBMC data
• Fig. 5: Analysis of gradient vector fields of COVID-19 data
• Fig. 6: Analysis of latent splicing space
• Fig. 6: Analysis of latent stability space

Data

Instructions on how to download the data can be found on the following notebooks:

• Download the PBMC data
• Download the COVID-19 data
• Download the LaManno data

Models and other data needed to run the notebooks can be found in the following Zenodo accessions:

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Package

To download and install GEDI, please visit here.

Preprint

Madrigal, A., Lu, T., Soto, L. M., & Najafabadi, H. S. (2023). A unified model for interpretable latent embedding of multi-sample, multi-condition single-cell data. bioRxiv, 2023-08.