Moderator: Michael Dondrup

gravatar for Michael Dondrup
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

<prev • 4,912 results • page 1 of 492 • next >
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Comment: C: How to add linear regression line and change the colors of my hexbin scatterplot
... 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 Dondrup45k
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Comment: 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 Dondrup45k
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Comment: C: Primer Design for amplifying complete viral genome
... 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 Dondrup45k
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Comment: C: How can implement ensembl gene annotation pipeline for my data?
... 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 Dondrup45k
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Comment: 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 Dondrup45k
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Comment: 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 Dondrup45k
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Answer: A: How can implement ensembl gene annotation pipeline for my data?
... 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 Dondrup45k
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Comment: 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 Dondrup45k
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Comment: C: Add RPKM values together for multiple different genes?
... 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 Dondrup45k
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Comment: C: EMBO | EMBL Symposium: Seeing is Believing - Imaging the Molecular Processes of
... I believe this is a bit strict to close this. ...
written 8 days ago by Michael Dondrup45k

Latest awards to Michael Dondrup

Epic Question 1 day ago, created a question with more than 10,000 views. For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Commentator 2 days ago, created a comment with at least 3 up-votes. For C: How To Analyse Epigenetics Data Using Bioinformatics Tools?
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: I Am Preparing A Course On Ngs: Any Suggestion ?
Student 5 days ago, asked a question with at least 3 up-votes. For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: I Am Preparing A Course On Ngs: Any Suggestion ?
Scholar 9 days ago, created an answer that has been accepted. For A: How to start a website with jbrowse to show sequencing data?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: I Am Preparing A Course On Ngs: Any Suggestion ?
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to start a website with jbrowse to show sequencing data?
Scholar 6 weeks ago, created an answer that has been accepted. For A: How To Split A Bam File By Chromosome
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How to start a website with jbrowse to show sequencing data?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Filter Polya/T And Other Repeats In Illumina Reads
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Filter Polya/T And Other Repeats In Illumina Reads
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: What Does Bwa'S '-N' Parameter Mean?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Filter Polya/T And Other Repeats In Illumina Reads
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: How To Analyse Epigenetics Data Using Bioinformatics Tools?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: I Am Preparing A Course On Ngs: Any Suggestion ?

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