Search
Question: find intersections of genomic regions with built-in genomic annotations for S.Cerevisiae
0
gravatar for vivianengoune
22 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 22 months ago • written 22 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 22 months ago by rcavalca130
0
gravatar for rcavalca
22 months ago by
rcavalca130
United States
rcavalca130 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 22 months ago by rcavalca130
0
gravatar for vivianengoune
22 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 22 months ago by vivianengoune0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 292 users visited in the last hour