there are plenty of experiments in GEO and elsewhere that were aligned to
mm8, although I don't know if you so much need the BSgenome package to deal
with them (i.e. as opposed to liftOver).    As recently as last year people
were still aligning to it


On Thu, Jun 21, 2012 at 5:43 PM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:

> I would prefer sacCer1 to be kept around; we have packaged data that
> was mapped to this version.  And it is small.
>
> I would suggest keeping mm8 around as well, but I am not working in
> mouse myself.  I don't know what the situation is in mouse, but plenty
> of people are still using hg18.  Perhaps it is the same for mouse.
>
> Kasper
>
> On Thu, Jun 21, 2012 at 4:37 PM, Hervé Pagès <hpages@fhcrc.org> wrote:
> > Hi there,
> >
> > Just packaged BSgenome.Rnorvegicus.UCSC.rn5 (Rat) and
> > BSgenome.Ggallus.UCSC.galGal4 (Chicken), and dropped them
> > into our BioC 2.11 (devel) repository. They should become
> > available via biocLite() within the next hour or so. Note
> > that only the source tarballs will be available for the moment
> > so Windows and Mac users will need to install with:
> >
> >  install.packages(..., type="source")
> >
> > BTW, if nobody still needs them, I'd like to stop supporting mm8
> > (from Feb. 2006) and sacCer1 (Oct. 2003) at some point. They've
> > both been superseded by newer assemblies: by mm9 and sacCer2 for
> > a while, and more recently by mm10 and sacCer3. The current plan
> > is that they will be part of the next release (Bioc 2.11, October
> > 2012) but will be removed from Bioc 2.12 (if nobody says anything
> > in the meantime).
> >
> > Thanks,
> > H.
> >
> > --
> > Hervé Pagès
> >
> > Program in Computational Biology
> > Division of Public Health Sciences
> > Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N, M1-B514
> > P.O. Box 19024
> > Seattle, WA 98109-1024
> >
> > E-mail: hpages@fhcrc.org
> > Phone:  (206) 667-5791
> > Fax:    (206) 667-1319
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> _______________________________________________
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>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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