Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • batel
    Junior Member
    • Feb 2015
    • 5

    #1

    Troubles installing ballgown

    Hi all,
    I have lots of BAM files and I want to use ballgown for differential ewxpression.
    I'm using the manuals (https://github.com/alyssafrazee/ballgown , http://master.bioconductor.org/packa...n/ballgown.pdf)
    in order to install it and use it..
    I have R version 3.1.2 and bioConductor version 3.0. The installation (from the README) seems fine, the last lines are:
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded
    * DONE (ballgown)

    The downloaded source packages are in
    ‘/tmp/RtmpNRWjaS/downloaded_packages’

    BUT, when I try to use ballgown() (just to see if it works), I get an error:
    Error: could not find function "ballgown"
    I tried also stattest() and it gave me the same error..
    I tried to use lines from the README and the manual but I got the same error.

    I believe I'm doing something wrong.. can someone help me understand what's going on?
    Thank you!!
    Batel
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142

    #2
    Did you load ballgown package before trying other commands?

    > library(ballgown)

    Ballgown installed using following commands:

    > source("http://bioconductor.org/biocLite.R")
    > biocLite("ballgown")

    Comment

    • batel
      Junior Member
      • Feb 2015
      • 5

      #3
      oh I'm ashamed. I had another troubles installing it earlier so "library" didn't help me than, and somehow I forgot use it after the installation worked..
      Thank you very much!!!

      Comment

      Latest Articles

      Collapse

      • SEQadmin2
        Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
        by SEQadmin2



        Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

        Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating
        ...
        10-14-2026, 09:55 AM
      • SEQadmin2
        New Genomics Technologies Take Aim at Long-Standing Limits
        by SEQadmin2


        Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

        We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing
        ...
        09-28-2026, 10:25 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by SEQadmin2, 10-22-2026, 11:13 AM
      0 responses
      24 views
      0 reactions
      Last Post SEQadmin2  
      Started by SEQadmin2, 10-22-2026, 10:48 AM
      0 responses
      20 views
      0 reactions
      Last Post SEQadmin2  
      Started by SEQadmin2, 10-15-2026, 10:52 AM
      0 responses
      36 views
      0 reactions
      Last Post SEQadmin2  
      Started by SEQadmin2, 10-14-2026, 05:39 AM
      0 responses
      42 views
      0 reactions
      Last Post SEQadmin2  
      Working...