User: Federico Marini

gravatar for Federico Marini
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5 years, 4 months ago
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Posts by Federico Marini

<prev • 33 results • page 1 of 4 • next >
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Comment: C: using limma for circular RNA analyses
... 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
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Comment: C: go_bp table in custom OrgDb package
... 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
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Comment: C: go_bp table in custom OrgDb package
... Will do, thanks. Federico ...
written 5 months ago by Federico Marini120
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Comment: C: go_bp table in custom OrgDb package
... 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
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Comment: C: DESeq2 - v1.18 different p-values from v1.20 (Is it minmu?)
... 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
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Comment: C: How can I get all installed Bioconductor packages?
... 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
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Comment: C: How can I get all installed Bioconductor packages?
... 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
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Answer: A: How can I get all installed Bioconductor packages?
... 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
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Answer: A: SPIA function error in ToPASeq
... 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
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Job: Bioinformatician/Biostatistician - Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Mainz, Germany
... The Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI) at the University Medical Center, is seeking a motivated Bioinformatician/Statistician (m/f) - Reference 50028764 The Division Biostatistics/Bioinformatics coordinates various biostatistical/bioinformatic supporting acti ...

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