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  • lavik17
    Member
    • Nov 2013
    • 10

    Visualizing number of hits on KEGG map

    Hi Everyone,
    I'm not sure this is the right place in SEQanswers for this question but I'll give it a go.
    I have a list of KO terms and for each of them I have the number of times this term was found in several samples. For example it would look something like this (tab delimited):

    kO:k0001 KO:k0002 KO:k0003 etc.
    Sample 1 10 12 14
    Sample 2 23 11 12
    Sample 3 12 14 15
    etc.
    I am looking for some automated/fast way of adding the number of hits information onto a KEGG pathway map, so it would show (maybe by colored boxes or gradient) how many hits were for each of KO term. I have the same type of file with EC hits if needed.

    I'm sure that there is something out there that can do this...
    Thanks !
  • lavik17
    Member
    • Nov 2013
    • 10

    #2
    I've found Pathview for R which seems like the right tool.

    But
    I still didn't manage to use it.
    I did run the tutorial pack that comes with it, but how do I make a list of KEGG pathways that I am interested in ? I can't find the right format of list/file for Pathview to read...
    Does anyone have any experience with this software?

    Comment

    • lavik17
      Member
      • Nov 2013
      • 10

      #3
      Still have errors running it.
      Does any know how to use it ?

      Comment

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