BSgenome packages for ce10 and panTro3 (was Re: BSgenome.Celegans.UCSC.cd10 for WS220)
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@herve-pages-1542
Last seen 1 day ago
Seattle, WA, United States
Hi Julie and other BSgenome users, I've just made 2 new BSgenome data packages, one for ce10 (Oct. 2010, WS220 assembly), and one for panTro3 (Oct. 2010, CGSC Build 2.1.3): BSgenome.Celegans.UCSC.ce10 BSgenome.Ptroglodytes.UCSC.panTro3 The data in both packages were downloaded from: http://hgdownload.cse.ucsc.edu/downloads.html Note that, strangely, ce10 is not listed in this table: http://genome.ucsc.edu/FAQ/FAQreleases.html#release1 The 2 new packages will become available for Bioc 2.11 users (Bioc devel) via biocLite() in less than 1 hour. Only the "source" packages are available for now. Windows and Mac users need to install with biocLite( ... , type="source"). Please let me know if you have any question or find any issue with those packages. Thanks! Cheers, H. On 05/07/2012 08:00 AM, Zhu, Lihua (Julie) wrote: > Herve, > > Hope all is well with you! Please let me know when the > BSgenome.Celegans.UCSC.cd10 for WS220 is available for use. > > Many thanks! > > Best regards, > > Julie > > On 4/20/12 5:08 PM, "Julie Zhu"<julie.zhu at="" umassmed.edu=""> wrote: > >> Herve, >> >> Great! Thanks so much for your kind help! >> >> Best regards, >> >> Julie >> >> >> On 4/20/12 4:04 PM, "Hervé Pagès"<hpages at="" fhcrc.org=""> wrote: >> >>> Hi Julie, >>> >>> On 04/20/2012 10:48 AM, Zhu, Lihua (Julie) wrote: >>>> Herve, >>>> >>>> Is it possible to add BSgenome.Celegans.UCSC.ce10 for WS220 in the >>>> Bioconductor release? Many thanks for your help! >>> >>> Sure. Given the number of sticky notes that are accumulating in front >>> my eyes every day, it might take me a few days though. Thanks for your >>> patience... >>> >>> Cheers, >>> H. >>> >>>> >>>> Best regards, >>>> >>>> Julie >>>> >>>> >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- 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 at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 4 months ago
United States
Herve, Thank you for making the packages! I really appreciate it! Best regards, Julie On 5/8/12 1:47 PM, "Hervé Pagès" <hpages at="" fhcrc.org=""> wrote: > Hi Julie and other BSgenome users, > > I've just made 2 new BSgenome data packages, one for ce10 (Oct. 2010, > WS220 assembly), and one for panTro3 (Oct. 2010, CGSC Build 2.1.3): > > BSgenome.Celegans.UCSC.ce10 > BSgenome.Ptroglodytes.UCSC.panTro3 > > The data in both packages were downloaded from: > > http://hgdownload.cse.ucsc.edu/downloads.html > > Note that, strangely, ce10 is not listed in this table: > > http://genome.ucsc.edu/FAQ/FAQreleases.html#release1 > > The 2 new packages will become available for Bioc 2.11 users > (Bioc devel) via biocLite() in less than 1 hour. Only the "source" > packages are available for now. Windows and Mac users need to install > with biocLite( ... , type="source"). > > Please let me know if you have any question or find any issue with > those packages. Thanks! > > Cheers, > H. > > On 05/07/2012 08:00 AM, Zhu, Lihua (Julie) wrote: >> Herve, >> >> Hope all is well with you! Please let me know when the >> BSgenome.Celegans.UCSC.cd10 for WS220 is available for use. >> >> Many thanks! >> >> Best regards, >> >> Julie >> >> On 4/20/12 5:08 PM, "Julie Zhu"<julie.zhu at="" umassmed.edu=""> wrote: >> >>> Herve, >>> >>> Great! Thanks so much for your kind help! >>> >>> Best regards, >>> >>> Julie >>> >>> >>> On 4/20/12 4:04 PM, "Hervé Pagès"<hpages at="" fhcrc.org=""> wrote: >>> >>>> Hi Julie, >>>> >>>> On 04/20/2012 10:48 AM, Zhu, Lihua (Julie) wrote: >>>>> Herve, >>>>> >>>>> Is it possible to add BSgenome.Celegans.UCSC.ce10 for WS220 in the >>>>> Bioconductor release? Many thanks for your help! >>>> >>>> Sure. Given the number of sticky notes that are accumulating in front >>>> my eyes every day, it might take me a few days though. Thanks for your >>>> patience... >>>> >>>> Cheers, >>>> H. >>>> >>>>> >>>>> Best regards, >>>>> >>>>> Julie >>>>> >>>>> >>>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at 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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