Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • crusty
    Junior Member
    • Feb 2015
    • 2

    #1

    What is the best clustering/visualization tools for RSEM data points?

    Hi, I am looking for simple tools to cluster/visualize transcriptomics data sets that are provided as a list of genes (contigs) with RSEM values assigned for each condition and put together as a table in the Excel spreadsheet. The laptop runs latest windows and doesn't have any bioinformatics packages installed.
    I would appreciate any help,
    Thanks
  • sarvidsson
    Senior Member
    • Jan 2015
    • 137

    #2
    I'm not aware of any free software that visualizes RNA-Seq counts - if you e.g. run the DESeq2 vst or rlog transform (http://www.bioconductor.org/packages....pdf#section.2) on the count tables, you could use good old MeV (http://www.tm4.org/mev.html)...

    Comment

    • crusty
      Junior Member
      • Feb 2015
      • 2

      #3
      MeV worked beautifully! Thanks, Sarvidsson!

      Comment

      Latest Articles

      Collapse

      • SEQadmin2
        16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
        by SEQadmin2




        NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification, detection...
        10-30-2026, 06:46 AM
      • 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

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by SEQadmin2, 10-28-2026, 09:57 AM
      0 responses
      39 views
      0 reactions
      Last Post SEQadmin2  
      Started by SEQadmin2, 10-28-2026, 09:51 AM
      0 responses
      23 views
      0 reactions
      Last Post SEQadmin2  
      Started by SEQadmin2, 10-22-2026, 11:13 AM
      0 responses
      73 views
      0 reactions
      Last Post SEQadmin2  
      Started by SEQadmin2, 10-22-2026, 10:48 AM
      0 responses
      48 views
      0 reactions
      Last Post SEQadmin2  
      Working...