Re: [galaxy-dev] Regarding galaxy wrappers: "lumi", "DESeq" "edgeR"
Hi Sachit, It's packaged up so it installs from the test toolshed directly via the admin interface of your test instance, but you'll need a good reliable network as there is a lot that gets downloaded and installed. Like other toolshed tools, it would be possible but not advisable to download and unpack the archive at http://testtoolshed.g2.bx.psu.edu/view/fubar/edger_test and install manually but your instance will need R 3.0.1 with bioconductor/edgeR/deseq/limma installed - if it's your first try, it will probably take some time and effort to read all the relevant docs to do that or the R/BioC mailing lists can provide assistance if you need it. The edgeR tool requires a count matrix (reads per sample per contig) as input which the htseq tool http://testtoolshed.g2.bx.psu.edu/view/fubar/htseq_bams_to_count_matrix will generate from any number of aligned bam/sam files and a GTF file with the appropriate gene model. Again, automatic installation from the toolshed is highly recommended, otherwise you'll need to manually install the tool and the dependencies. Note that edgeR requires replicate samples in each comparison group so the absolute minimum is 4 bam files as input to the count matrix maker. p values from analyses without replicates are not interpretable in any biologically meaningful way and are meaningless in terms of the usual frequentist interpretation in my opinion. On Mon, Jul 8, 2013 at 4:28 PM, Sachit Adhikari wrote: > Sorry about that Ross. I would try your wrapper of "edgeR" and would > happily report you the bug. Can you make me the link of Galaxy Test > Toolshed? > > Thanks, > > Sachit > > > On Mon, Jul 8, 2013 at 11:51 AM, Ross wrote: > >> (Sachit, please don't cross-post to the dev and user lists?) >> There's a beta version of an edgeR/deseq/voom wrapper and a companion >> htseq based count matrix maker in the test toolshed statistics section >> owned by me - fubar. Definitely not quite ready for production but >> installable and I'd appreciate feedback from anyone brave enough to try >> them out. Best installed on a test instance you plan on destroying because >> the R 3.0 dependency is about to swap over to Bjorns better one - should be >> done later this week when I get some time. >> >> Be warned it takes a long time to auto-install - 10-15 minutes or so on >> my laptop. >> >> >> On Mon, Jul 8, 2013 at 3:36 PM, Sachit Adhikari < >> sachit.techner...@gmail.com> wrote: >> >>> Hi, >>> >>> These are the R libraries. Have anyone written a wrapper for these >>> libraries "lumi", "DESeq" "edgeR"? >>> >>> Thanks, >>> >>> Sachit >>> >>> ___ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> >> >> >> -- >> Ross Lazarus MBBS MPH; >> Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 >> http://scholar.google.com/citations?hl=en&user=UCUuEM4J >> > > -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4J ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Regarding galaxy wrappers: "lumi", "DESeq" "edgeR"
Sorry about that Ross. I would try your wrapper of "edgeR" and would happily report you the bug. Can you make me the link of Galaxy Test Toolshed? Thanks, Sachit On Mon, Jul 8, 2013 at 11:51 AM, Ross wrote: > (Sachit, please don't cross-post to the dev and user lists?) > There's a beta version of an edgeR/deseq/voom wrapper and a companion > htseq based count matrix maker in the test toolshed statistics section > owned by me - fubar. Definitely not quite ready for production but > installable and I'd appreciate feedback from anyone brave enough to try > them out. Best installed on a test instance you plan on destroying because > the R 3.0 dependency is about to swap over to Bjorns better one - should be > done later this week when I get some time. > > Be warned it takes a long time to auto-install - 10-15 minutes or so on my > laptop. > > > On Mon, Jul 8, 2013 at 3:36 PM, Sachit Adhikari < > sachit.techner...@gmail.com> wrote: > >> Hi, >> >> These are the R libraries. Have anyone written a wrapper for these >> libraries "lumi", "DESeq" "edgeR"? >> >> Thanks, >> >> Sachit >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > > > -- > Ross Lazarus MBBS MPH; > Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 > http://scholar.google.com/citations?hl=en&user=UCUuEM4J > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Regarding galaxy wrappers: "lumi", "DESeq" "edgeR"
(Sachit, please don't cross-post to the dev and user lists?) There's a beta version of an edgeR/deseq/voom wrapper and a companion htseq based count matrix maker in the test toolshed statistics section owned by me - fubar. Definitely not quite ready for production but installable and I'd appreciate feedback from anyone brave enough to try them out. Best installed on a test instance you plan on destroying because the R 3.0 dependency is about to swap over to Bjorns better one - should be done later this week when I get some time. Be warned it takes a long time to auto-install - 10-15 minutes or so on my laptop. On Mon, Jul 8, 2013 at 3:36 PM, Sachit Adhikari wrote: > Hi, > > These are the R libraries. Have anyone written a wrapper for these > libraries "lumi", "DESeq" "edgeR"? > > Thanks, > > Sachit > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4J ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
