Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Question: Multi omics dataset analyses, where to start? And methods to use?

    I have been given a dataset containing the following information: Species data was collected from Daphnia magna, the data consists of transcriptomic data (RNA-Seq) and polar metabolomic data (DIMS). This information was collected under 2 conditions, 1 = treatment with an unknown metal ion. 2 = treatment with an unknown metal nanoparticle. Data was collected over three time points; early (hours), intermediate, late (days). The experiment was repeated for multiple biological replicates. The task we have been given is to use statistics, machine learning, and bioinformatics knowledge to look for genes and metabolites that co-vary across conditions and in response to perturbations in an animal system.

    The data provided is in tsv format and contains the following: - Information on genes monitored including gene ID, gene family information, and information on functions. - Similar information for metabolites including empirical information, functional information and peaks in measurements. - Two other tsv files describing the change in gene expression over time for each individual and condition and another for metabolite data describing the same changes. This is all the information and instruction we have been given, we have 3 days to analyse the dataset. Could anyone suggest where to start looking for a method to start analysing this data? As we have covered limited machine learning, so our knowledge is limited at this time. Any advice on methods / resources would be greatly appreciated.

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, 03-27-2024, 06:37 PM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-27-2024, 06:07 PM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
53 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
69 views
0 likes
Last Post seqadmin  
Working...
X