Moderator: Michael Dondrup
Michael Dondrup ♦ 45k
- Reputation:
- 44,700
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- Trusted
- Location:
- Bergen, Norway
- Website:
- https://licebase.org/
- Last seen:
- 55 seconds ago
- Joined:
- 8 years, 8 months ago
- Email:
- m*******@gmail.com
PhD in bioinformatics. Currently Researcher at the Sea Lice Research Centre, responsible for LiceBase, an infrastructure for genomic resources of sea lice, and analysis of genomics data from emerging genomes.
Posts by Michael Dondrup
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... Hi, I don't see any connection to bioinformatics in your post, except that biologist and bioinformaticians might appreciate nice graphics. Then, this is the wrong forum to learn pure R stuff. ...
written 1 day ago by
Michael Dondrup ♦ 45k
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C: Molecular dynamic simulation
... Hello Sarah Diana!
We believe that this post does not fit the main topic of this site.
No longer relevant.
For this reason we have closed your question. This allows us to keep the site focused
on the topics that the community can help with.
If you disagree please tell us why in a reply below, ...
written 2 days ago by
Michael Dondrup ♦ 45k
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... Comment from the wet lab: Make sure you use a suitable polymerase for the resulting fragment size, normal Taq polymerase can possibly not amplify this fragment size. ...
written 2 days ago by
Michael Dondrup ♦ 45k
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... Possibly not all of them, also what you can get depends on the evidence data you have. Prediction of de-novo non-coding genes is often pretty bad except for tRNA anyway. I recommend you start with a feasible approach first, e.g. looking at the MAKER docs and install some of its dependencies, then pr ...
written 3 days ago by
Michael Dondrup ♦ 45k
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C: feature extraction from SNPs in R
... Please consider that your mentor might have an inadequate grasp of the problem as well. As Ram and Wouter have said earlier, these p-value cutoffs are inadequate and especially the 0.8 limit is completely arbitrary. ...
written 3 days ago by
Michael Dondrup ♦ 45k
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C: feature extraction from SNPs in R
... Not really. possibly you are looking for something like eQTL analysis, but I think you should first force your supervisor to be more clear about the project setup, otherwise it's just a waste of time by guess work. Also, if you got p-values already, these are most likely already the best way to esti ...
written 3 days ago by
Michael Dondrup ♦ 45k
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... There is currently no easy way or stream-lined way to install the Ensembl annotation pipeline locally, therefore I do not recommend to even attempt this as a beginner. This doesn't mean it has to stay like this, Ensembl and EBI have been working on a distributed [Ensembl infrastructure within Elixir ...
written 3 days ago by
Michael Dondrup ♦ 45k
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C: feature extraction from SNPs in R
... First, you need a proper classification task, that means at least two classes to sort items into. You need to know what are your items and what are your classes. Then, you can decide what your features could be.
You will need a training and test set, that means you need data associating class and it ...
written 3 days ago by
Michael Dondrup ♦ 45k
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... To add an explanation to this: To condense gene expression profiles of duplicated genes into a single value and present *only* this is inadequate, because duplication can lead to neofunctionalization and functional diversification and can also lead to diversification of gene regulation (e.g. [Kleinj ...
written 7 days ago by
Michael Dondrup ♦ 45k
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... I believe this is a bit strict to close this. ...
written 8 days ago by
Michael Dondrup ♦ 45k
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For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
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For C: How To Analyse Epigenetics Data Using Bioinformatics Tools?
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For A: How to start a website with jbrowse to show sequencing data?
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created a question with more than 1,000 views.
For Closing Aug. 15th: PhD Position in Computational Biology (4 years), Evolution of Gene Regulation, University of Bergen, Norway
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For Closing Aug. 15th: PhD Position in Computational Biology (4 years), Evolution of Gene Regulation, University of Bergen, Norway
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For Closing Aug. 15th: PhD Position in Computational Biology (4 years), Evolution of Gene Regulation, University of Bergen, Norway
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For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
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8 weeks ago,
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For Closing Aug. 15th: PhD Position in Computational Biology (4 years), Evolution of Gene Regulation, University of Bergen, Norway
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For A: I Am Preparing A Course On Ngs: Any Suggestion ?
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