## User: Federico Marini

Reputation:
120
Status:
Trusted
Location:
Germany
Last seen:
4 days ago
Joined:
5 years, 4 months ago
Email:
m******@uni-mainz.de

#### Posts by Federico Marini

<prev • 33 results • page 1 of 4 • next >
1
168
views
1
... To add on Aaron's answer: - circRNA detection can depend heavily on the library prep method for RNA-seq: do you have ribo-depleted samples? - circRNA quantification can indeed deliver somewhat lower counts (or estimated counts, if you followed the sailfish-cir pipeline?), so it may happen that som ...
written 5 months ago by Federico Marini120
1
185
views
1
... Sorry for the confusion in pointing towards limmaquick2pca2go . I checked now and noticed goana has built in support for a few species, but custom annotation packages can still be provided. The problem is then once you'd need the egGO2ALLEGS, and it can be that if it is built with that metho ...
written 5 months ago by Federico Marini120
1
185
views
1
... Will do, thanks. Federico ...
written 5 months ago by Federico Marini120
1
185
views
1
... Hi James and @psutton, here I am. In the specific case of pca2go I am calling an underlying routine that is based on the good old topGO package. That package, in turn, expects to provide one of the three main ontologies to compute the enriched functions. I might be wrong, but there is currentl ...
written 5 months ago by Federico Marini120
1
329
views
1
... Have a look here, there is a reference to that parameter. https://github.com/mikelove/DESeq2/blob/a24c0bd71fb4a621a7c0772ca00825db5af5c69b/NEWS#L26   ...
written 12 months ago by Federico Marini120
3
360
views
3
... I think the OP can be quite satisfied with the material over here, the latest one is nice & compact indeed   ...
written 13 months ago by Federico Marini120
3
360
views
3
... I think I wrote my piece of code before the nice sessioninfo came out, and sticked to that since it was working :D ...
written 13 months ago by Federico Marini120
3
360
views
3
... Hi ishenweiyan, this is part of a script I use to document every now and then the packages I have stored by major R version change # using package_info for the extra info delivered ### -> you might need to change the lib.loc according to system/version allpkgs <- (devtools:::package_info(ro ...
written 13 months ago by Federico Marini120
1
195
views
1
... AFAIK ToPASeq does not load SPIA, so it seems normal that the function is not available. library(SPIA) could do the job? ...
written 14 months ago by Federico Marini120
0
644
views
5 follow
0