[BioC] ggbio 1.12.0 autoplot() with txdb example is broken

Thu Apr 24 00:38:11 CEST 2014

Dang it, forgot again to send with my @jhsph.edu account. See below again >.<

On the email topic, is it possible to be subscribed with 2 emails
accounts to the BioC mailing list but only get emails with one? I
believe that I have to choose to either get the daily digest or get a
single for every message sent. If not, I'll probably just drop my
@jhsph.edu subscription and re-subscribe with the new @jhu.edu mail I
got (our university is pushing these mails).

On Wed, Apr 23, 2014 at 6:32 PM, Leonardo Collado Torres
<lcollado at jhu.edu> wrote:
> Hi Dan,
>
> I got RSwitch to work with a second installation of R 3.1. Basically,
> I downloaded the leopard tarball, expanded it, renamed the folder 3.1
> to 3.1patched (which is the version I downloaded, but well, anything
> except for 3.1 would work), compressed it again, and then expanded it
> at the root location.
>
> So it would be something like this:
>
> wget http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1-branch-snowleopard-sa-x86_64.tar.gz
> tar -xvf R-*gz
> mv Library/Frameworks/R.framework/Versions/3.1
> Library/Frameworks/R.framework/Versions/3.1patched
> tar -cvzf Rlib.tgz Library
> sudo tar fvxz Rlib.tgz -C /
>
> Then used RSwitch, and was able to install BioC-devel.
>
> I might try out your `renv` at a different time. It's great to know
> that it exists =)
>
> Cheers,
> Leo
>
>
> On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin <tengfei.yin at sbgenomics.com> wrote:
>> Hi Dan,
>>
>> It works like a charm, thanks!
>>
>> I use your method, then I changed /Library/Framework/ folder and R.Framework
>> folder ownership to myself so I don't have to sudo it, then I just add alias
>> to "emacs2" and "emacs3" to run your renv to switch the R first. This solves
>> my problem.
>>
>> Try to customize variable for R hooks in emacs as alternative solution, but
>> may need more time.
>>
>> Thanks again!
>>
>> Tengfei
>>
>>
>> On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>>
>>> Hi Tengfei,
>>>
>>> ----- Original Message -----
>>> > From: "Tengfei Yin" <tengfei.yin at sbgenomics.com>
>>> > To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
>>> > Cc: "Bioconductor mailing list" <bioconductor at r-project.org>,
>>> > lcollado at jhu.edu
>>> > Sent: Wednesday, April 23, 2014 11:01:18 AM
>>> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken
>>> >
>>> >
>>> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all on the R 3.1?
>>>
>>> Yes, install two copies of R 3.1 and switch between them.
>>>
>>> > And do some sort of switch for bioc? The website you send to me also
>>> > have a R-devel build, my plan is to install bioc 3.0 on R-devel and
>>> > bioc 2.14 on R 3.1, and do some tricks with emacs for R only to
>>> > switch bioc, so that I could debug and maintain released and devel
>>> > version.
>>>
>>> PLEASE don't use R-devel at all.
>>>
>>> Just use R-3.1.0.
>>>
>>> You can use the Rswitch app but as you point out it won't work within
>>> emacs.
>>>
>>> This is what I do:
>>>
>>> Every time I download a new version of R, I run its installer. The
>>> installer always puts it in
>>>
>>> /Library/Frameworks/R.framework
>>>
>>> So after I install each version of R, I rename the R.framework directory
>>> to something like
>>> R.framework.bioc214_snowleopard
>>>
>>> And then I make a symlink from R.framework.bioc214_snowleopard to
>>> R.framework.
>>>
>>> I have a little script at https://github.com/dtenenba/renv which lets me
>>> see what the various installed Rs are:
>>>
>>> $ renv
>>> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0
>>> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0
>>> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0
>>> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0
>>> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0
>>>
>>> This tells me that the currently active R is nicknamed "releaseMav" (this
>>> means there is a link from /Library/Frameworks/R.framework.releaseMav to
>>> /Library/Frameworks/R.framework. It shows the versions, svn revisions,
>>> dates, and architectures of each version. (darwin10.8.0 is Snow Leopard;
>>> darwin13.1.0 is Mavericks).
>>>
>>> Note that in my nomenclature devel means BioC devel, not R-devel.
>>>
>>> So if I wanted to switch to the "develSL" version I would do:
>>>
>>> sudo renv develSL
>>>
>>> HTH
>>> Dan
>>>
>>>
>>>
>>> >
>>> >
>>> >
>>> > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum < dtenenba at fhcrc.org >
>>> > wrote:
>>> >
>>> >
>>> >
>>> > Hi Tengfei,
>>> >
>>> > ----- Original Message -----
>>> > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com >
>>> >
>>> > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org >
>>> > > Cc: "Bioconductor mailing list" < bioconductor at r-project.org >,
>>> > > lcollado at jhu.edu
>>> >
>>> > > Sent: Wednesday, April 23, 2014 10:46:02 AM
>>> > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is
>>> > > broken
>>> > >
>>> > >
>>> >
>>> > > Thanks a lot Dan! it's clear to me now, sorry that I am still a
>>> > > newbie to OSX ... I got R-devel running and I will try Rswitcher, I
>>> > > also want to do that switch easily in emacs too.
>>> > >
>>> > >
>>> >
>>> > You don't want to use R-devel. Both BioC release (2.14) and BioC
>>> > devel (3.0) are meant to work with R-3.1.0, the released version of
>>> > R.
>>> >
>>> > I think the Rswitch app just sets a symbolic link, so you should be
>>> > able to do that within emacs. Run it and see what it does to
>>> > /Library/Frameworks/R.framework.
>>> >
>>> > Dan
>>> >
>>> >
>>> > >
>>> > > cheers
>>> > >
>>> > >
>>> > > Tengfei
>>> > >
>>> > >
>>> > >
>>> >
>>> >
>>> > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < dtenenba at fhcrc.org
>>> > > >
>>> > > wrote:
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> > > ----- Original Message -----
>>> > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com >
>>> > >
>>> > > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org >
>>> > > > Cc: "Bioconductor mailing list" < bioconductor at r-project.org >,
>>> > > > lcollado at jhu.edu
>>> > > > Sent: Wednesday, April 23, 2014 9:24:42 AM
>>> > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is
>>> > > > broken
>>> > > >
>>> > > >
>>> > >
>>> > > > Hi Dan,
>>> > > >
>>> > > >
>>> > > > So you mean I install R 3.1 for snow leopard and it should work?
>>> > >
>>> > > Yes.
>>> > >
>>> > >
>>> > >
>>> > > ? Is
>>> > > > there a way to build from source using biocLite, like type =
>>> > > > "source", this is what I got
>>> > > >
>>> > > >
>>> > > >
>>> > > > > library(BiocInstaller)
>>> > > > Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite for
>>> > > > help
>>> > > > > biocLite("GenomicRanges")
>>> > > > BioC_mirror: http://bioconductor.org
>>> > > > Using Bioconductor version 2.14 (BiocInstaller 1.14.1), R version
>>> > > > 3.1.0.
>>> > > > Installing package(s) 'GenomicRanges'
>>> > > >
>>> > > >
>>> > > > package ‘GenomicRanges’ is available as a source package but not
>>> > > > as
>>> > > > a
>>> > > > binary
>>> > > >
>>> > > >
>>> > > > Warning message:
>>> > > > package ‘GenomicRanges’ is not available (for R version 3.1.0)
>>> > > >
>>> > > >
>>> > > > Just wondering is there a solution without re-install R for snow
>>> > > > leopard. And what's the plan for maverick?
>>> > > >
>>> > >
>>> > > You can do
>>> > > biocLite("GenomicRanges", type="source")
>>> > >
>>> > > but you need to have the appropriate compilers, etc.
>>> > >
>>> > > I *STRONGLY* recommend using the Snow Leopard build. You can have
>>> > > multiple installations of R on your Mac and switch between them
>>> > > using Rswitch ( http://r.research.att.com/#other ) or another easy
>>> >
>>> >
>>> > > mechanism.
>>> > >
>>> > > We are building packages for Mavericks now, we just have to resolve
>>> > > a
>>> > > few build issues and test the resulting packages, we still hope to
>>> > > have them available by the end of the month. But since you can
>>> > > install the Snow Leopard build without needing to remove your
>>> > > Mavericks build, you should do that.
>>> > >
>>> > > Dan
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> > > >
>>> > > > Thanks
>>> > > >
>>> > > >
>>> > > > Tengfei
>>> > > >
>>> > > >
>>> > > >
>>> > > >
>>> > > >
>>> > > >
>>> > > >
>>> > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum <
>>> > > > dtenenba at fhcrc.org
>>> > > > > wrote:
>>> > > >
>>> > > >
>>> > > > Hi Tengfei,
>>> > > >
>>> > > >
>>> > > > ----- Original Message -----
>>> > > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com >
>>> > > > > To: lcollado at jhu.edu
>>> > > > > Cc: bioconductor at r-project.org
>>> > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM
>>> > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example
>>> > > > > is
>>> > > > > broken
>>> > > > >
>>> > > > > btw, based on the error, let me try to debug it.
>>> > > > >
>>> > > > >
>>> > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin
>>> > > > > < tengfei.yin at sbgenomics.com >wrote:
>>> > > > >
>>> > > > > > Hi Leonardo,
>>> > > > > >
>>> > > > > > Frankly speaking, the vignette is still in progress, and
>>> > > > > > there
>>> > > > > > are
>>> > > > > > some
>>> > > > > > known bugs in ggbio I need to fix (still trying to find a
>>> > > > > > time
>>> > > > > > to
>>> > > > > > do that
>>> > > > > > ... ), I am recently trying to install R 3.1 and Bioc 2.14 on
>>> > > > > > my
>>> > > > > > new MBP
>>> > > > > > with OSX 10.9, but fails, probably binary build is not ready
>>> > > > > > for
>>> > > > > > maverick
>>> > > > > > yet, maybe available by the end of April?
>>> > > > > >
>>> > > > > > Thanks for reporting the bug, I will keep you posted on this
>>> > > > > > when
>>> > > > > > I
>>> > > > > > successfully get it on my laptop and start fixing the
>>> > > > > > problems.
>>> > > > > >
>>> > > >
>>> > > > You can install the Snow Leopard build of R and should have no
>>> > > > problems, binary packages are available for that version. It will
>>> > > > run fine on Mavericks.
>>> > > >
>>> > > > Dan
>>> > > >
>>> > > >
>>> > > >
>>> > > >
>>> > > > > > cheers
>>> > > > > >
>>> > > > > > Tengfei
>>> > > > > >
>>> > > > > >
>>> > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres <
>>> > > > > > lcollado at jhsph.edu > wrote:
>>> > > > > >
>>> > > > > >> Hello Tengfei + bioc list,
>>> > > > > >>
>>> > > > > >> From
>>> > > > > >>
>>> > > > > >> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/inst/doc/ggbio.pdf
>>> > > > > >> page 4 (complied on april 11 2014), the following example
>>> > > > > >> loads
>>> > > > > >> to
>>> > > > > >> an
>>> > > > > >> error as shown below. I wasn't seeing this error before
>>> > > > > >> (aka,
>>> > > > > >> last
>>> > > > > >> week). The only guess that comes to mind is the recent
>>> > > > > >> update
>>> > > > > >> to
>>> > > > > >> GenomicRanges (1.16.2) although that doesn't seem to be
>>> > > > > >> related
>>> > > > > >> from
>>> > > > > >> the traceback() output, well... maybe it's related to the
>>> > > > > >> ignore.strand = TRUE part as described in the error.
>>> > > > > >>
>>> > > > > >> I'll create a GitHub issue just for completeness.
>>> > > > > >>
>>> > > > > >> Thank you,
>>> > > > > >> Leonardo
>>> > > > > >>
>>> > > > > >> > library(ggbio)
>>> > > > > >> ## Removed the output, nothing out of ordinary
>>> > > > > >>
>>> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene)
>>> > > > > >> ## Removed the output
>>> > > > > >>
>>> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
>>> > > > > >> > data(genesymbol, package = "biovizBase")
>>> > > > > >> > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"])
>>> > > > > >> Aggregating TranscriptDb...
>>> > > > > >> Parsing transcripts...
>>> > > > > >> Parsing exons...
>>> > > > > >> Parsing cds...
>>> > > > > >> Parsing utrs...
>>> > > > > >> ------exons...
>>> > > > > >> ------cdss...
>>> > > > > >> ------introns...
>>> > > > > >> ------utr...
>>> > > > > >> aggregating...
>>> > > > > >> Done
>>> > > > > >> Constructing graphics...
>>> > > > > >> Error in sapply(listData, function(Xi) extends(class(Xi),
>>> > > > > >> elementTypeX)) :
>>> > > > > >> error in evaluating the argument 'X' in selecting a method
>>> > > > > >> for
>>> > > > > >> function 'sapply': Error in unlist(range(ranges(x.n,
>>> > > > > >> ignore.strand
>>> > > > > >> =
>>> > > > > >> TRUE))) :
>>> > > > > >> error in evaluating the argument 'x' in selecting a method
>>> > > > > >> for
>>> > > > > >> function 'unlist': Error in .local(x, ...) : unused argument
>>> > > > > >> (ignore.strand = TRUE)
>>> > > > > >>
>>> > > > > >> > traceback()
>>> > > > > >> 15: sapply(listData, function(Xi) extends(class(Xi),
>>> > > > > >> elementTypeX))
>>> > > > > >> 14: .updateCompressedList(X, lapply_CompressedList(X, FUN,
>>> > > > > >> ...))
>>> > > > > >> 13: endoapply(obj.lst, function(x) {
>>> > > > > >> if (!is.null( group.name )) {
>>> > > > > >> if (!group.selfish) {
>>> > > > > >> x.n <- split(x, values(x)[, group.name ])
>>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand =
>>> > > > > >> TRUE)))
>>> > > > > >> irs.new <- resize(irs, fix = fix, width =
>>> > > > > >> width(irs) +
>>> > > > > >> extend.size)
>>> > > > > >> irs.new <- sort(irs.new)
>>> > > > > >> .lvs <- disjointBins(irs.new)
>>> > > > > >> values(x)$stepping <-
>>> > > > > >> .lvs[as.character(values(x)[,
>>> > > > > >> group.name ])]
>>> > > > > >> x
>>> > > > > >> }
>>> > > > > >> else {
>>> > > > > >> values(x)$stepping <-
>>> > > > > >> as.numeric(as.factor(values(x)[,
>>> > > > > >> group.name ]))
>>> > > > > >> x
>>> > > > > >> }
>>> > > > > >> }
>>> > > > > >> else {
>>> > > > > >> irs <- ranges(x)
>>> > > > > >> values(x)$stepping <-
>>> > > > > >> as.numeric(disjointBins(resize(irs,
>>> > > > > >> fix = "center", width = width(irs) +
>>> > > > > >> extend.size)))
>>> > > > > >> x
>>> > > > > >> }
>>> > > > > >> })
>>> > > > > >> 12: endoapply(obj.lst, function(x) {
>>> > > > > >> if (!is.null( group.name )) {
>>> > > > > >> if (!group.selfish) {
>>> > > > > >> x.n <- split(x, values(x)[, group.name ])
>>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand =
>>> > > > > >> TRUE)))
>>> > > > > >> irs.new <- resize(irs, fix = fix, width =
>>> > > > > >> width(irs) +
>>> > > > > >> extend.size)
>>> > > > > >> irs.new <- sort(irs.new)
>>> > > > > >> .lvs <- disjointBins(irs.new)
>>> > > > > >> values(x)$stepping <-
>>> > > > > >> .lvs[as.character(values(x)[,
>>> > > > > >> group.name ])]
>>> > > > > >> x
>>> > > > > >> }
>>> > > > > >> else {
>>> > > > > >> values(x)$stepping <-
>>> > > > > >> as.numeric(as.factor(values(x)[,
>>> > > > > >> group.name ]))
>>> > > > > >> x
>>> > > > > >> }
>>> > > > > >> }
>>> > > > > >> else {
>>> > > > > >> irs <- ranges(x)
>>> > > > > >> values(x)$stepping <-
>>> > > > > >> as.numeric(disjointBins(resize(irs,
>>> > > > > >> fix = "center", width = width(irs) +
>>> > > > > >> extend.size)))
>>> > > > > >> x
>>> > > > > >> }
>>> > > > > >> })
>>> > > > > >> 11: .local(obj, ...)
>>> > > > > >> 10: addStepping(gr, group.name = "tx_id", group.selfish =
>>> > > > > >> FALSE,
>>> > > > > >> fix = "start", extend.size = es)
>>> > > > > >> 9: addStepping(gr, group.name = "tx_id", group.selfish =
>>> > > > > >> FALSE,
>>> > > > > >> fix = "start", extend.size = es)
>>> > > > > >> 8: .local(data, ...)
>>> > > > > >> 7: (function (data, ...)
>>> > > > > >> standardGeneric("geom_alignment"))(data = <S4 object of
>>> > > > > >> class
>>> > > > > >> "TranscriptDb">,
>>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment",
>>> > > > > >> stat = "identity", names.expr = "tx_name", label = TRUE,
>>> > > > > >> which = <S4 object of class "GRanges">, list())
>>> > > > > >> 6: (function (data, ...)
>>> > > > > >> standardGeneric("geom_alignment"))(data = <S4 object of
>>> > > > > >> class
>>> > > > > >> "TranscriptDb">,
>>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment",
>>> > > > > >> stat = "identity", names.expr = "tx_name", label = TRUE,
>>> > > > > >> which = <S4 object of class "GRanges">, list())
>>> > > > > >> 5: do.call(geom_alignment, args.res)
>>> > > > > >> 4: do.call(geom_alignment, args.res)
>>> > > > > >> 3: .local(object, ...)
>>> > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"])
>>> > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"])
>>> > > > > >>
>>> > > > > >>
>>> > > > > >> > sessionInfo()
>>> > > > > >> R version 3.1.0 (2014-04-10)
>>> > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>> > > > > >>
>>> > > > > >> locale:
>>> > > > > >> [1]
>>> > > > > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>> > > > > >>
>>> > > > > >> attached base packages:
>>> > > > > >> [1] parallel stats graphics grDevices utils datasets
>>> > > > > >> methods base
>>> > > > > >>
>>> > > > > >> other attached packages:
>>> > > > > >> [1] XVector_0.4.0
>>> > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0
>>> > > > > >> GenomicFeatures_1.16.0
>>> > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0
>>> > > > > >> GenomicRanges_1.16.2
>>> > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3
>>> > > > > >> ggbio_1.12.0
>>> > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0
>>> > > > > >>
>>> > > > > >> loaded via a namespace (and not attached):
>>> > > > > >> [1] BatchJobs_1.2 BBmisc_1.5
>>> > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0
>>> > > > > >> Biostrings_2.32.0
>>> > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6
>>> > > > > >> BSgenome_1.32.0 cluster_1.15.2
>>> > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7
>>> > > > > >> dichromat_2.0-0 digest_0.6.4
>>> > > > > >> [16] fail_1.2 foreach_1.4.2
>>> > > > > >> Formula_1.1-1
>>> > > > > >> GenomicAlignments_1.0.0 grid_3.1.0
>>> > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2
>>> > > > > >> Hmisc_3.14-4
>>> > > > > >> iterators_1.0.7 labeling_0.2
>>> > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31
>>> > > > > >> munsell_0.4.2 plyr_1.8.1
>>> > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1
>>> > > > > >> RCurl_1.95-4.1 reshape2_1.2.2
>>> > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4
>>> > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2
>>> > > > > >> [41] splines_3.1.0 stats4_3.1.0
>>> > > > > >> stringr_0.6.2
>>> > > > > >> survival_2.37-7 tools_3.1.0
>>> > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1
>>> > > > > >> zlibbioc_1.10.0
>>> > > > > >> >
>>> > > > > >>
>>> > > > > >
>>> > > > > >
>>> > > > > >
>>> > > > > > --
>>> > > > > > Tengfei Yin, PhD
>>> > > > > > Seven Bridges Genomics
>>> > > > > > sbgenomics.com
>>> > > > > > 625 Mt. Auburn St. Suite #208
>>> > > > > > Cambridge, MA 02138
>>> > > > > > (617) 866-0446
>>> > > > > >
>>> > > > >
>>> > > > >
>>> > > > >
>>> > > > > --
>>> > > > > Tengfei Yin, PhD
>>> > > > > Seven Bridges Genomics
>>> > > > > sbgenomics.com
>>> > > > > 625 Mt. Auburn St. Suite #208
>>> > > > > Cambridge, MA 02138
>>> > > > > (617) 866-0446
>>> > > > >
>>> > > > > [[alternative HTML version deleted]]
>>> > > > >
>>> > > > > _______________________________________________
>>> > > > > 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
>>> > > > >
>>> > > >
>>> > > >
>>> > > >
>>> > > >
>>> > > > --
>>> > > >
>>> > > >
>>> > > > Tengfei Yin, PhD
>>> > > > Seven Bridges Genomics
>>> > > > sbgenomics.com
>>> > > > 625 Mt. Auburn St. Suite #208
>>> > > > Cambridge, MA 02138
>>> > > > (617) 866- 0446
>>> > > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> > > --
>>> > >
>>> > >
>>> > > Tengfei Yin, PhD
>>> > > Seven Bridges Genomics
>>> > > sbgenomics.com
>>> > > 625 Mt. Auburn St. Suite #208
>>> > > Cambridge, MA 02138
>>> > > (617) 866- 0446
>>> > >
>>> >
>>> >
>>> >
>>> >
>>> > --
>>> >
>>> >
>>> > Tengfei Yin, PhD
>>> > Seven Bridges Genomics
>>> > sbgenomics.com
>>> > 625 Mt. Auburn St. Suite #208
>>> > Cambridge, MA 02138
>>> > (617) 866- 0446
>>> >
>>
>>
>>
>>
>> --
>> Tengfei Yin, PhD
>> Seven Bridges Genomics
>> sbgenomics.com
>> 625 Mt. Auburn St. Suite #208
>> Cambridge, MA 02138
>> (617) 866-0446