tabula-muris-vignettes

What's this?

This is a collection of analysis vignettes showcasing the possibilities and challenges provided by recent organism-wide murine single-cell sequencing projects.

There are three datasets, two from CZ Biohub's Tabula Muris and one from the Guo lab's Mouse Cell Atlas. They each cover 12-20 different organs, and together provide different technical profiles in terms of cell sorting, lysis, barcoding, and library preparation.

We believe that these datasets provide sufficient breadth and diversity to serve as model systems for:

• cell type annotation and reannotation at various levels of ontological depth
• building and validating cell type classifiers
• manifold alignment and batch-effect-aware analyses
• assessing the variability in gene expression of cell types present in many organs, like immune cells, endothelial cells, and epithelial cells.
• measuring sex differences in gene expression
• measuring the variability in biological claims (like which genes are differentially expressed between populations) to be expected between different studies

How to use

Instructions on how to download the datasets are in the data directory in the repo. Given those instructions (and sufficient installed dependencies), all notebooks in vignettes should run.

How to contribute

Contributed posts are welcome! We are working out the details of publication (likely through a blog driven by this repo), but the basic workflow to make a post is:

1. Make a new branch
2. Put all notebooks and generated html in the vignettes folder
3. Submit a PR for review

Vignettes

• The Hazards of Regression: What happens when you try to remove technical confounders that are correlated with cell type?