tinyatlas is a tiny cell atlas in an easily digestable format, useful for marking known cell types in commonly sequenced organisms when looking at single-cell RNA-seq data.
We've concluded from looking at many single-cell experiments that markers for cell types are not always useful for classifying cell types from single-cell RNA sequencing data. Sometimes markers will not be as specific to a specific cell type as thought or are not expressed at a high enough level to be picked up reliably by single-cell RNA sequencing. Markers that work well for FACS sorting may not be useful when looking at the RNA expression. This repository is a compilation of what we think are good markers for the cell types we've encountered, across a variety of organisms.
If you have data of your own to contribute of any kind, please do.
These lists were originally compiled by Mike Steinbaugh here (https://docs.google.com/spreadsheets/d/1vGNU2CCxpaoTCLvzOxK1hf5gjULrf2-CpgCp9bOfGJ0) and (https://docs.google.com/spreadsheets/d/1qA5ktYeimNGpZF1UPSQZATbpzEqgyxN6daoMOjv6YYw). We moved them here to give better access to the community so we can work together on improving them. Moving to git also lets us address specific versions by git hashes, so we can be sure which versions of the markers we have used.
2018-10-19: Zebrafish Cell cycle and cell type genes added using homology information against Homo sapiens.
Script found at code folder. It uses biomaRt and only one2one orthology type and high orthology confidence.
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2019-04-19: Found typo in code for gene2Drerio.Rmd that was saving the wrong object. Corrected and uploaded the correct file.
3d6a07d... Update README.md