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Question: Request: Add Macaca fascicularis genome to BSgenome
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gravatar for amy.klegarth
2.5 years ago by
United States
amy.klegarth0 wrote:

I realize Rhesus macaques - Macaca mulatta are already on BSGenomes - but the long-tailed macaque genome is also available and they are also widely used as major biomedical model.  As such, I wanted to see if it might be a candidate for being added to the BSGenome list.  

The genome can be found here:

http://www.ncbi.nlm.nih.gov/genome/776

 

My lab is also working with several parasites of macaques including Blastocystis spp and Plasmodium spp that coinfect humans - I'm going to be compiling my own BSGenome packages for those, but common parasites like those are good options for more permanent additions to BSGenomes I'd be happy to provide links.

Cheers,

  Amy

ADD COMMENTlink modified 2.5 years ago by Hervé Pagès ♦♦ 13k • written 2.5 years ago by amy.klegarth0
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gravatar for Hervé Pagès
2.5 years ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

Hi Amy,

Sorry for the delay. Just added the BSgenome.Mfascicularis.NCBI.5.0 package to the release and devel versions of BioC. Should become available in a couple of hours or so.

As for a BSgenome data package containing common parasites, I feel the use case is maybe too narrow to justify its inclusion to our data annotation repos but, to be honnest, I've no idea how much demand there is for something like that. I'll be happy to reconsider if other people think this is something they would find useful.

Cheers,

H.

ADD COMMENTlink written 2.5 years ago by Hervé Pagès ♦♦ 13k
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