Visualization of GEO stats

rnabioco / scRNA-seq-Cell-Ref-Matrix

A reference matrix atlas of all single cell RNA-seq data on NCBI GEO for mice and humans

https://rnabioco.github.io/scRNA-seq-Cell-Ref-Matrix/

4 stars 1 forks source link

Visualization of GEO stats #49

Open raysinensis opened 4 years ago

raysinensis commented 4 years ago

For next week's meeting, we'll again talk about the short comment article idea. Let's brainstorm the best way to make the code to pull data and plot as reproducible as possible.

kriemo commented 4 years ago

I agree. I also think we should consider looking through datasets listed in a curated list of single cell experiments and annotating if they have sufficient metadata to generate a reference.

This preprint is a great starting point with an easy to parse google doc. preprint: https://www.biorxiv.org/content/10.1101/742304v2

database: https://docs.google.com/spreadsheets/d/1En7-UV0k0laDiIfjFkdn7dggyR7jIk3WH8QgXaMOZF0/edit#gid=0

raysinensis commented 4 years ago

We could also start think about comparing the different data sources, see if any of them are better (don't think so...) GEO https://singlecell.broadinstitute.org/single_cell https://www.ebi.ac.uk/gxa/sc/home etc