search

dviraran / SingleR

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

incorportaing custom datasets #5

Open gosuzombie opened 6 years ago

gosuzombie commented 6 years ago

Is there a feature to add custom expression data to the algorithm? ex if I have tumor signatures?

dviraran commented 6 years ago

Hi,

The SingleR pipeline is not based on signatures, rather on full expression profiles of pure cell types. You can see details on generating a reference dataset here: http://comphealth.ucsf.edu/sample-apps/SingleR/SingleR_create.html

If you are still interested in testing gene signatures, you can try out the function calculateSignatures.

Hope this helps.

Best, Dvir