search

Irrationone / cellassign

Automated, probabilistic assignment of cell types in scRNA-seq data
Other
192 stars 82 forks source link

How to assign cell population with t-SNE? #38

Closed jrnick7 closed 5 years ago

jrnick7 commented 5 years ago

Hi, In the vignette, I didn't find how to use this package to annotate cell population in a t-SNE plot? Do you have any idea to deal with that?

kieranrcampbell commented 5 years ago

You would use the scRNA-seq count data as input to cellassign as per the vignette, get cell assignments, then compute the t-SNE representation (using e.g. plotTSNE in scater), and colour the points by the cell assignment. The visualization part (t-SNE) is separate from the cell assignment part that uses the gene expression data.

jrnick7 commented 5 years ago

Thanks. I'll try that. By the way, with no offense, have you compared your package with Alona (panglaodb)? I just start learning scRNA-seq, so I'm wondering which method I should follow.