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Question: find intersections of genomic regions with built-in genomic annotations for S.Cerevisiae
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gravatar for vivianengoune
20 months ago by
vivianengoune0 wrote:

Hello

i have already use annotatr package for H.sapiens, but now i want to find intersections of genomic regions with built-in genomic annotations for S.Cerevisiae and i want to know how i have to do it. 

thanks

Viviane

 

ADD COMMENTlink modified 20 months ago • written 20 months ago by vivianengoune0

Hi Viviane,

Thanks for using annotatr. At the moment you need to provide S. Cerevisiae annotations as custom annotations with the read_annotations() function. I am currently working on a more general function to convert any GRanges resource in the AnnotationHub  package into an annotation for use in annotatr. If S. Cerevisiae annotations are in the Hub as GRanges, you'll be able to use those. I'll update this thread when that function is implemented, tested, and released.

ADD REPLYlink written 20 months ago by rcavalca120
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gravatar for rcavalca
20 months ago by
rcavalca120
United States
rcavalca120 wrote:

Hi Viviane,

Thanks for using annotatr. At the moment you need to provide S. Cerevisiae annotations as custom annotations with the read_annotations() function. I am currently working on a more general function to convert any GRanges resource in the AnnotationHub  package into an annotation for use in annotatr. If S. Cerevisiae annotations are in the Hub as GRanges, you'll be able to use those. I'll update this thread when that function is implemented, tested, and released.

ADD COMMENTlink written 20 months ago by rcavalca120
0
gravatar for vivianengoune
20 months ago by
vivianengoune0 wrote:

Hello

Thank you for the info

annotatr could also be more interesting if we are able to build up annotation for ncRNA, not only lncRNA which didn't work pretty well when i used it.

thanks

Viviane

ADD COMMENTlink written 20 months ago by vivianengoune0
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