search

bhklab / PharmacoGx

R package to analyze large-scale pharmacogenomic datasets.
http://pharmacodb.pmgenomics.ca
GNU General Public License v3.0
64 stars 26 forks source link

Which version of ConnectivityMap can be accessed? #131

Open AnjaliS1 opened 1 year ago

AnjaliS1 commented 1 year ago

Hi I just wanted to clarify as to which ConnectivityMap version is held within the database in the package? Is it CMap1 or CMap2?

iamsinht commented 1 year ago

Hello -

The CMAP PSet in PharmacoGx is from Lamb et al 2006. To clarify nomenclature, I believe this is the second (larger) version of the Affymetrix-based Connectivity Map from Lamb 2006. The CMAP PSet is not the L1000 Connectivity Map published in Subramanian 2017. Are you trying to get access to specific Connectivity Map data?

Cheers, Ian

AnjaliS1 commented 1 year ago

Hi Ian,

Ah I see, thank you for the information. I found the package really good to use and was hoping to access ConnectivityMap through R rather than the web browser that they have available. Yes, I was hoping to access the L1000 ConnectivityMap, which I believe is what is currently available through the CMap web browser.

Thanks, Anjali