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Tutorial: Epigenomics RoadMap Project files now accessible via AnnotationHub
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gravatar for Sonali Arora
23 months ago by
Sonali Arora350
United States
Sonali Arora350 wrote:

Files from Epigenomics RoadMap Project have been added to AnnotationHub.

This vignette inside AnnotationHub gives you a quick tour on how to access these files  via the Hub with some examples.

Please let us know if you'd like any other files to be added to the Hub from the same project or another.

 

Thanks and Regards,

Sonali 
 

Hi Sonali, are there any plans to add access to the raw data (ie consolidated and unconsolidated tagAlign files) through AnnotationHub? As far as I can tell, this info is not indexed in a publicly accessible way and the easiest method currently is just to parse the file names from the web server HTML. Also, does AnnotationHub provide any methods to download files to disk rather than straight into R? Obviously for large BAM-type files working in memory is not always an option.

ADD REPLYlink modified 16 months ago • written 16 months ago by Malcolm Perry30
1

cache(hub["AH12345"]) retrieves the resource(s) to local disk (if necessary) and returns the path. Mostly large files are not read in to R, but returned in a format that can be queried for relevant information (as with the fasta file vignette example).

ADD REPLYlink written 16 months ago by Martin Morgan ♦♦ 19k

Dear Sonali,

I just posted a question regarding some Roadmap files: AnnotationHub: confusing pValue/qValue for (some) Roadmap records

Many thanks in advance,
Kevin

ADD REPLYlink written 12 months ago by kevin.rue200

I've responded to this question at AnnotationHub: confusing pValue/qValue for (some) Roadmap records

Valerie

ADD REPLYlink written 12 months ago by Valerie Obenchain ♦♦ 6.1k
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