[Bioc-devel] Masked version of BSgenome.Hsapiens.NCBI.GRCh38?

[Hervé Pagès]

On 02/08/2015 11:23 PM, Hervé Pagès wrote:
> Hi Ulrich,
>
> I was not sure about how much demand there is for the masked BSgenome
> packages in general so I was just waiting for someone to ask. Note that
> the masks are typically generated from data available at UCSC so it
> sounds that it's time to make BSgenome.Hsapiens.NCBI.hg38 and
> BSgenome.Hsapiens.NCBI.hg38.masked available.

I meant BSgenome.Hsapiens.UCSC.hg38 and 
BSgenome.Hsapiens.UCSC.hg38.masked, sorry.

H.

>
> I'll prepare the 2 packages in the next couple of weeks and post back
> here when they are ready for download.
>
> Cheers,
> H.
>
> On 02/06/2015 06:13 AM, Ulrich Bodenhofer wrote:
>> Hi,
>>
>> The latest human genome build GRCh38 has been around in Bioconductor for
>> some while (package BSgenome.Hsapiens.NCBI.GRCh38). As far as I can
>> tell, however, there is currently no package that provides easy access
>> to masked/unmasked regions in the genome (like there is a .masked
>> version that wraps BSgenome objects into MaskedBSgenome objects for many
>> other genomes, e.g. there is BSgenome.Hsapiens.UCSC.hg19.masked for
>> hg19). Here is my question: does anybody have plans to include  a
>> package BSgenome.Hsapiens.NCBI.GRCh38.masked (or under a different name)
>> into Bioconductor 3.1? At least I could not find anything in the current
>> development branch.
>>
>> Thanks and best regards,
>> Ulrich
>>
>>
>> ------------------------------------------------------------------------
>> *Dr. Ulrich Bodenhofer*
>> Associate Professor
>> Institute of Bioinformatics
>>
>> *Johannes Kepler University*
>> Altenberger Str. 69
>> 4040 Linz, Austria
>>
>> Tel. +43 732 2468 4526
>> Fax +43 732 2468 4539
>> bodenhofer at bioinf.jku.at <mailto:bodenhofer at bioinf.jku.at>
>> http://www.bioinf.jku.at/ <http://www.bioinf.jku.at>
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
Hervé Pagès

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