Re: [galaxy-user] Cuffdiff statistical calculations are inconsistent?

Hi Jeremy, The header of the Cuffdiff tool page says it is version 0.0.5 Is there a way, or setting, on Cuffdiff 2.0 to revert the parameters to be more similar to Cuffdiff 1.3? Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe

[galaxy-user] How to connect to private instance of galaxy from another computer

Dear Galaxy, I am running an instance of Galaxy on my computer through localhost:8080/ and am wondering if I can use this on my laptop? I basically don't want to be at the computer at the same time and don't want to upload files to and from my laptop but just use the galaxy interface to work wi

Re: [galaxy-user] [devteam-bioc] User dropdown menu as galaxy input file

Hi Alex, On Tue, Mar 12, 2013 at 6:25 PM, Maintainer wrote: > Good afternoon, > > I have a query that I hope you can help me with. I am using RGalaxy, and have > successfully built a number of useful tools for my instance of Galaxy, using > this in R. At the moment, all these tools are using

[galaxy-user] User dropdown menu as galaxy input file

Good afternoon, I have a query that I hope you can help me with. I am using RGalaxy, and have successfully built a number of useful tools for my instance of Galaxy, using this in R. At the moment, all these tools are using the default galaxy input file, following the example tools. Is there a w

[galaxy-user] Knowing who is currently logged into your system

Hello All, I was wondering if there is a way to know all the users logged into your local galaxy server? Thanks, -Akshay Choche ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public

Re: [galaxy-user] Cuffdiff statistical calculations are inconsistent?

This is likely due to the upgrade from Cufflinks 1.3.x to Cufflinks 2.0.x; Cufflinks 2.0 introduced a new algorithm for Cuffdiff in particular. You can read about these changes on the website: http://cufflinks.cbcb.umd.edu/ (and there's a manuscript describing the changes as well). You might co

Re: [galaxy-user] Cuffdiff statistical calculations are inconsistent?

We are having the exact same issue, on the main server and our (recent) cloud instances. Were some of the hidden Cuffdiff parameters modified since fall 2012? Cheers, Mo Heydarian On Mar 13, 2013 11:02 AM, "Jenna Smith" wrote: > Hi, > > I'll preface my concern by saying that I'm a novice to Cuf

[galaxy-user] Cuffdiff statistical calculations are inconsistent?

Hi, I'll preface my concern by saying that I'm a novice to Cufflinks. Back in September, I performed a Cuffdiff analysis comparing a wild-type and mutant condition. The analysis returned ~800 transcripts differentially regulated between the two with statistical significance. Recently, I've reru