search

dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
263 stars 98 forks source link

What's the difference between singler$singler[[1]] and [[2]] #91

Open jrnick7 opened 5 years ago

jrnick7 commented 5 years ago

Hi, Firstly, thanks for developing such great tools for annotating Single-cell cluster.

However, I do confuse with the subset of singler$singler[[1]] and [[2]], I tried to plot-stne with singler$singler[[1]] or [[2]] as input, they look exactly same. So I'm wondering what's the difference between [[1]] and [[2]]? If they are different, how to decide to use which one?

dviraran commented 5 years ago

Thanks!

Each one is based on a different reference dataset. In human [[1]] is annotations based on HPCA, and [[2]] is annotations based on Blueprint-Encode. In mouse [[1]] is based on Immgen and [[2]] is based on a RNA-seq samples.

How to decide is a different question. Each reference has its strength and weaknesses, and it really depends on the application.

Best, Dvir