Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • A comparison tree for multiple RNA-seqs

    Is there a program that can compare 20 RNA-seqs (with different treatments in the same cell line) to one another and determine which samples are the most similar and which are most different? It would be kind of like a phylogenetic comparison... or an RNA-seq BLAST.

    I'm not sure what his would even be called so searching for it is hard.

    Thanks

  • #2
    BTW, I don't want to do a gene expression comparison but a whole sample to whole sample.

    Comment


    • #3
      Do you mean a hierarchical clustering? You could do a heatmap with hierarchical clustering easily in R, for instance.

      Comment


      • #4
        R has a ton of packages for this ranging from simple regression models to more complicated machine learning algorithms for clustering. What type of comparison do you want to do?
        If you're not familiar with R, you could give this program a shot:

        Here's the paper describing it:

        Comment


        • #5
          Thanks for these answers. I will try them.

          Comment


          • #6
            Have a look at the section on sample clustering and PCA in the new DESeq vignette.

            Comment


            • #7
              what would you recommend for plotting heatmaps of multiple conditions?
              I really appreciate DEseq for pairwise comparison but having more than 10 conditions make analysis a bit problematic especially when it comes to heatmaps, and comparison between samples

              Comment


              • #8
                How about doing MDS plot? It can be easily done in R.

                Comment


                • #9
                  not enough I was asked for heatmaps, to reveal nice clusters and so...
                  this is not that straightforward having multiple conditions in DEseq analysis

                  Comment

                  Latest Articles

                  Collapse

                  • seqadmin
                    Exploring the Dynamics of the Tumor Microenvironment
                    by seqadmin




                    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
                    07-08-2024, 03:19 PM
                  • seqadmin
                    Exploring Human Diversity Through Large-Scale Omics
                    by seqadmin


                    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
                    06-25-2024, 06:43 AM

                  ad_right_rmr

                  Collapse

                  News

                  Collapse

                  Topics Statistics Last Post
                  Started by seqadmin, Today, 06:53 AM
                  0 responses
                  11 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 07-10-2024, 07:30 AM
                  0 responses
                  32 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 07-03-2024, 09:45 AM
                  0 responses
                  203 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 07-03-2024, 08:54 AM
                  0 responses
                  213 views
                  0 likes
                  Last Post seqadmin  
                  Working...
                  X