Closed harimchun closed 1 year ago
Hi @harimchun
There are currently two versions of DoRothEA. In the original package we store the old one (dorothea::dorothea_hs
) while in OmniPath we store the new one (which we call from decoupleR with decoupleR::get_dorothea
).
We recommend using the new one through decoupleR. In the future release of BioC we are going to update the dorothea
package so that the two versions match.
Thanks! I would use decoupleR::get_dorothea
Have a great day.
Hi, I am using decoupleR with my scRNA-seq data.
While inferring transcription factor activities using the DoRothEA, I found discrepancies in the database size.
If I download TF-Target information (Confidence level: A, B, C, D) using the DoRothEA library using the R code below,
I can get 361 unique TF information.
However, when I download TF-Target information (Confidence level: A, B, C, D) using the decoupleR library using the R code below,
I can get 643 unique TF information.
Also, column names are different between the two databases. I don't know why these discrepancies occurred.
In this case, which database should I use to infer the transcription factor activities?