DiffBind annotation
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Rory Stark ★ 4.4k
@rory-stark-5741
Last seen 1 day ago
CRUK, Cambridge, UK
Hi Igor- We avoided adding annotation to DiffBind because of the other packages that specialize in this. They don't take a DiffBind object directly, but you can always retrieve any peak set as a GRanges object, which is commonly used in Bioconductor packages. The main packages I use for annotation and gene set enrichment are ChIPpeakAnno and chipenrich. Peaksets are returned as GRanges objects by default by dba.peakset() (with bRetrieve=TRUE), dba.report() (for differentially bound peaks), and dba.overlap() (for peaks that do or don't overlap between peak sets; you can also use dbaPlotVenn() with bReturnPeaksets=TRUE). Cheers- Rory On 11/09/2014 21:22, "Dolgalev, Igor" <igor.dolgalev at="" nyumc.org=""> wrote: >Hello. > >I am getting started with DiffBind. I am really enjoying all the options >it provides. Unfortunately, it does not seem to do any annotation. For >example, it would be great to get the closest gene or distance to TSS/TTS >for the binding sites. I know there are tools available for this purpose. >Is there a specific one that you would recommend and that would integrate >with DiffBind (if it could take DBA object directly, for example)? > >Any assistance would be much appreciated. > >Thank you very much. > >Igor >
Annotation ChIPpeakAnno DiffBind chipenrich • 1.7k views
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