What happened to GenomicFeatures::spliceGraph?

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Ryan C. Thompson ★ 7.9k

@ryan-c-thompson-5618

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Icahn School of Medicine at Mount Sinai…

Hi all, As of BioC 2.10 (GenomicFeatures version 1.8.3), there was a spliceGraph function in the GenomicFeatures package, along with a vignette on how to use it, as seen here: http://www.bioconductor.org/packages/2.10/bioc/html/GenomicFeatures.ht ml However, in BioC 2.11 (GenomicFeatures 1.10.1) and higher, this function and its associated vignette appear to have disappeared. Can anyone shed some light on what has happened to this function? -Ryan Thompson

GenomicFeatures GenomicFeatures • 1.8k views

ADD COMMENT • link updated 11.9 years ago by Tim Triche ★ 4.2k • written 11.9 years ago by Ryan C. Thompson ★ 7.9k

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Tim Triche ★ 4.2k

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the SpliceGraph and SpliceGrapher packages took over that functionality On Thu, Feb 21, 2013 at 2:39 PM, Ryan C. Thompson <rct@thompsonclan.org>wrote: > Hi all, > > As of BioC 2.10 (GenomicFeatures version 1.8.3), there was a spliceGraph > function in the GenomicFeatures package, along with a vignette on how to > use it, as seen here: http://www.bioconductor.org/** > packages/2.10/bioc/html/**GenomicFeatures.html<http: www.bioconduct="" or.org="" packages="" 2.10="" bioc="" html="" genomicfeatures.html=""> > > However, in BioC 2.11 (GenomicFeatures 1.10.1) and higher, this function > and its associated vignette appear to have disappeared. Can anyone shed > some light on what has happened to this function? > > -Ryan Thompson > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]

ADD COMMENT • link 11.9 years ago Tim Triche ★ 4.2k

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On Thu, Feb 21, 2013 at 5:42 PM, Tim Triche, Jr. <tim.triche at="" gmail.com=""> wrote: > the SpliceGraph and SpliceGrapher packages took over that functionality Which are presumably only available via svn at the moment? I see that SpliceGraph is in svn and not on the devel package list -- I can't find SplieGrapher anywhere, tho. Maybe you mean SplicingGraphs? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

ADD REPLY • link 11.9 years ago Steve Lianoglou ★ 13k

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yes, that On Thu, Feb 21, 2013 at 2:55 PM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > On Thu, Feb 21, 2013 at 5:42 PM, Tim Triche, Jr. <tim.triche@gmail.com> > wrote: > > the SpliceGraph and SpliceGrapher packages took over that functionality > > Which are presumably only available via svn at the moment? > > I see that SpliceGraph is in svn and not on the devel package list -- > I can't find SplieGrapher anywhere, tho. > > Maybe you mean SplicingGraphs? > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]

ADD REPLY • link 11.9 years ago Tim Triche ★ 4.2k

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Ok, so it looks like this splice graph functionality is currently in limbo. If I wanted to use it right now with the current release of BioC, could I just use the old spliceGraph function from the previous GenomicFeatures version? I figure I could get it working by taking the R files from the old version, prefixing a few things with "GenomicFeatures::", and then sourcing the files. On 02/21/2013 03:05 PM, Tim Triche, Jr. wrote: > yes, that > > > On Thu, Feb 21, 2013 at 2:55 PM, Steve Lianoglou > <mailinglist.honeypot@gmail.com> <mailto:mailinglist.honeypot@gmail.com>> wrote: > > On Thu, Feb 21, 2013 at 5:42 PM, Tim Triche, Jr. > <tim.triche@gmail.com <mailto:tim.triche@gmail.com="">> wrote: > > the SpliceGraph and SpliceGrapher packages took over that > functionality > > Which are presumably only available via svn at the moment? > > I see that SpliceGraph is in svn and not on the devel package list -- > I can't find SplieGrapher anywhere, tho. > > Maybe you mean SplicingGraphs? > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > <http: cbio.mskcc.org="" %7elianos="" contact=""> > > > > > -- > /A model is a lie that helps you see the truth./ > / > / > Howard Skipper > <http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]

ADD REPLY • link 11.9 years ago Ryan C. Thompson ★ 7.9k

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On 02/21/2013 04:43 PM, Ryan C. Thompson wrote: > Ok, so it looks like this splice graph functionality is currently in > limbo. If I wanted to use it right now with the current release of BioC, > could I just use the old spliceGraph function from the previous > GenomicFeatures version? I figure I could get it working by taking the R > files from the old version, prefixing a few things with > "GenomicFeatures::", and then sourcing the files. it would be better to download and install from svn, for your version of R, e.g., for Bioc 2.11 / R-2.15.2 svn co https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/R packs/SpliceGraph R CMD INSTALL SpliceGraph Martin > > > On 02/21/2013 03:05 PM, Tim Triche, Jr. wrote: >> yes, that >> >> >> On Thu, Feb 21, 2013 at 2:55 PM, Steve Lianoglou >> <mailinglist.honeypot at="" gmail.com="">> <mailto:mailinglist.honeypot at="" gmail.com="">> wrote: >> >> On Thu, Feb 21, 2013 at 5:42 PM, Tim Triche, Jr. >> <tim.triche at="" gmail.com="" <mailto:tim.triche="" at="" gmail.com="">> wrote: >> > the SpliceGraph and SpliceGrapher packages took over that >> functionality >> >> Which are presumably only available via svn at the moment? >> >> I see that SpliceGraph is in svn and not on the devel package list -- >> I can't find SplieGrapher anywhere, tho. >> >> Maybe you mean SplicingGraphs? >> >> -steve >> >> -- >> Steve Lianoglou >> Graduate Student: Computational Systems Biology >> | Memorial Sloan-Kettering Cancer Center >> | Weill Medical College of Cornell University >> Contact Info: http://cbio.mskcc.org/~lianos/contact >> <http: cbio.mskcc.org="" %7elianos="" contact=""> >> >> >> >> >> -- >> /A model is a lie that helps you see the truth./ >> / >> / >> Howard Skipper >> <http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> > > > [[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 > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

ADD REPLY • link 11.9 years ago Martin Morgan 25k

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Ok, I will try it out and see how things go. Thanks for the clarification. On Feb 21, 2013 6:37 PM, "Martin Morgan" <mtmorgan@fhcrc.org> wrote: > On 02/21/2013 04:43 PM, Ryan C. Thompson wrote: > >> Ok, so it looks like this splice graph functionality is currently in >> limbo. If I wanted to use it right now with the current release of BioC, >> could I just use the old spliceGraph function from the previous >> GenomicFeatures version? I figure I could get it working by taking the R >> files from the old version, prefixing a few things with >> "GenomicFeatures::", and then sourcing the files. >> > > it would be better to download and install from svn, for your version of > R, e.g., for Bioc 2.11 / R-2.15.2 > > svn co https://hedgehog.fhcrc.org/**bioconductor/branches/RELEASE_** > 2_11/madman/Rpacks/SpliceGraph<https: hedgehog.fhcrc.org="" bioconduct="" or="" branches="" release_2_11="" madman="" rpacks="" splicegraph=""> > R CMD INSTALL SpliceGraph > > Martin > > >> >> On 02/21/2013 03:05 PM, Tim Triche, Jr. wrote: >> >>> yes, that >>> >>> >>> On Thu, Feb 21, 2013 at 2:55 PM, Steve Lianoglou >>> <mailinglist.honeypot@gmail.**com <mailinglist.honeypot@gmail.com=""> >>> <mailto:mailinglist.honeypot@**gmail.com<mailinglist.honeypot@gmai l.com="">>> >>> wrote: >>> >>> On Thu, Feb 21, 2013 at 5:42 PM, Tim Triche, Jr. >>> <tim.triche@gmail.com <mailto:tim.triche@gmail.com="">> wrote: >>> > the SpliceGraph and SpliceGrapher packages took over that >>> functionality >>> >>> Which are presumably only available via svn at the moment? >>> >>> I see that SpliceGraph is in svn and not on the devel package list >>> -- >>> I can't find SplieGrapher anywhere, tho. >>> >>> Maybe you mean SplicingGraphs? >>> >>> -steve >>> >>> -- >>> Steve Lianoglou >>> Graduate Student: Computational Systems Biology >>> | Memorial Sloan-Kettering Cancer Center >>> | Weill Medical College of Cornell University >>> Contact Info: http://cbio.mskcc.org/~lianos/**contact<http: cbio.mskcc.org="" ~lianos="" contact=""> >>> <http: cbio.mskcc.org="" %**7elianos="" contact<http:="" cbio.mskcc.="" org="" %7elianos="" contact=""> >>> > >>> >>> >>> >>> >>> -- >>> /A model is a lie that helps you see the truth./ >>> / >>> / >>> Howard Skipper >>> <http: cancerres.**aacrjournals.org="" content="" 31="" 9="" **1173.full.pdf<="" http:="" cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> >>> > >>> >> >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]

ADD REPLY • link 11.9 years ago Ryan C. Thompson ★ 7.9k

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