Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Obtaining gene sets for GSEA

    Hi All,

    I work with Bacillus subtilis and I want to perform some GSEA on an RNA-seq data set. Looking at the literature, I've seen that it is very much possible to do this. I know that gene sets can be constructed as well, but I'm not super great at automation and it seems like it would require a massive amount of time to do something like that manually.

    In some of the literature I've read, I've seen that gene sets could be obtained from KEGG. However, browsing the website, I'm not certain how gene sets could be extracted from KEGG.

    Can anyone help me in figuring out how to obtain gene sets for GSEA?

    Thanks!

  • #2
    Hi,

    I'm not sure what you have now. But if you have a list of differentially expressed genes with their fold change, such as the results from edgeR or DESeq2 package, I think the package `clusterProfiler` is good for you to do GO/GESA/KEGG directly. You could find their detailed manual here -> http://yulab-smu.top/clusterProfiler-book/chapter1.html.

    best

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:37 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    49 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X