Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Correlating/clustering RNA-seq with ChIP-seq data?

    Hi everyone,

    I have RNA-seq data from adipocytes, where a certain gene, that is involved in heterochromatin, is knocked out. I would like to correlate/cluster this dataset with another dataset, where we have ChIP-seq for H3K9me3.

    Basically, I would like to see if those genes that are upregulated in my knockout samples are the one that are enriched for H3K9me3.

    I have tried to search the forum here and have read several posts about the topic, but I am still not sure how to go about it and what packages to use.

    Thanks a lot! Appreciate your help.

    // Kevin

  • #2
    I know the TargetCaller package for R, but this is mainly for transcription factors. Whether it is suited for Histon ChIP-data you have to test.

    Comment


    • #3
      Have a look at the "Integrative analysis of epigenetics and gene expression" section of the Repitools manual. The heatmap plot is what you want to use.

      Comment


      • #4
        There's also the Rcade package in Bioconductor (R-based analysis of ChIP-seq And Differential Expression)...

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Best Practices for Single-Cell Sequencing Analysis
          by seqadmin



          While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
          06-06-2024, 07:15 AM
        • seqadmin
          Latest Developments in Precision Medicine
          by seqadmin



          Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

          Somatic Genomics
          “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
          05-24-2024, 01:16 PM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 07:24 AM
        0 responses
        9 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 06-13-2024, 08:58 AM
        0 responses
        11 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 06-12-2024, 02:20 PM
        0 responses
        16 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 06-07-2024, 06:58 AM
        0 responses
        184 views
        0 likes
        Last Post seqadmin  
        Working...
        X