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Moderator: Michael Dondrup

gravatar for Michael Dondrup
Reputation:
41,820
Status:
Trusted
Location:
Bergen, Norway
Website:
https://licebase.org/
Last seen:
7 minutes ago
Joined:
7 years, 3 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 • 4,461 results • page 1 of 447 • next >
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Comment: C: How and what are the steps for performing RNAseq Time point analysis 3 biologica
... Another comment: are you sure that your protocol is not strand specific? `-s no -r pos -t exon -f bam -s no` also you have doubled the parameter, be careful when trying out different combinations, to specify each parameter only once to avoid confusion, like in `-s no -r pos -t exon -f bam -s yes`, ...
written 7 minutes ago by Michael Dondrup ♦ 42k
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Comment: C: How and what are the steps for performing RNAseq Time point analysis 3 biologica
... How does STAR distinguish and group biological and technical replicates? This is an interesting example, because if that works, it is not clear from the documentation how to achieve this, and should be clarified. From the manual: --readFilesIn default: Read1 Read2 string(s): paths to ...
written 26 minutes ago by Michael Dondrup ♦ 42k
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Comment: C: Is it possible to retrieve this paper from any links or website?
... Hello vchris_ngs! We believe that this post does not fit the main topic of this site. Welcome to the beauty of closed-access publishing, unfortunately, this is nothing the community can help you with. If the paper was open-access (e.g. CC-BY) we could share it with you, but we can not without cop ...
written 6 hours ago by Michael Dondrup ♦ 42k
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Comment: C: How to annotate only selected genes on a heatmap
... fixed, thank you ...
written 3 days ago by Michael Dondrup ♦ 42k
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Comment: C: How to annotate only selected genes on a heatmap
... Sorry, drawing lines is a bit more difficult. How about something like this: heatmap.2(x, labRow = labRow, rowsep = c(9:10), sepwidth = c(0.05,0.05), sepcolor = 'blue') You just have to find your gene of interest in the dendrogram order. ...
written 3 days ago by Michael Dondrup ♦ 42k
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Answer: A: How to annotate only selected genes on a heatmap
... The easy way: use Row-labels and set all but those you want to show to empty string: data(mtcars) x <- as.matrix(mtcars) labRow <- c(row.names(x)[1], rep('', length(row.names(x))-1)) # take just the first name, here you can choose the ones you like heatmap.2(x, labRow = labRo ...
written 3 days ago by Michael Dondrup ♦ 42k
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Comment: C: How to annotate only selected genes on a heatmap
... Hi BioBing, this looks like a quite complex workflow for what OP wants to achieve. I am not doubting that it works, even though it is not possible to reproduce, but could you explain what it actually is at the core that displays only a selection of gene ids (e.g. setting them to NULL or empty string ...
written 3 days ago by Michael Dondrup ♦ 42k
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Comment: C: Column Regex Find And Replace
... Ah, it's a [Galaxy tool right][1]? [1]: http://%20https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=77ef66b907800659&tool_config=database%2Fcommunity_files%2F000%2Frepo_932%2Fregex_tabular.xml&changeset_revision=9ea374bb0350 ...
written 4 days ago by Michael Dondrup ♦ 42k
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Answer: C: Column Regex Find And Replace
... So you want to extract the gi number? I think those have deprecated. Anyway the regex in perl would be something like `/gi|(\d+)|/` I don't know what Column Regex Find And Replace means, it is not a software, I guess. ...
written 4 days ago by Michael Dondrup ♦ 42k
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Comment: C: Column Regex Find And Replace
... Interesting example, regarding "stealth viruses" see https://www.biostars.org/p/99057/ ...
written 4 days ago by Michael Dondrup ♦ 42k

Latest awards to Michael Dondrup

Good Answer 9 days ago, created an answer that was upvoted at least 5 times. For A: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
Appreciated 10 days ago, created a post with more than 5 votes. For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
Scholar 22 days ago, created an answer that has been accepted. For A: Protein Back Translation For Aneides Flavipunctatus
Great Question 4 weeks ago, created a question with more than 5,000 views. For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Comparing Alignments In An Iterative Process With Perl
Scholar 7 weeks ago, created an answer that has been accepted. For A: Protein Back Translation For Aneides Flavipunctatus
Scholar 7 weeks ago, created an answer that has been accepted. For A: Protein Back Translation For Aneides Flavipunctatus
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Comparing Alignments In An Iterative Process With Perl
Scholar 7 weeks ago, created an answer that has been accepted. For A: Protein Back Translation For Aneides Flavipunctatus
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Comparing Alignments In An Iterative Process With Perl
Scholar 7 weeks ago, created an answer that has been accepted. For A: mirDeep2 using bowtie vs. bwa - why do more aligned reads yield less miRNA
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: Why Don'T We Use Binary Format?
Scholar 11 weeks ago, created an answer that has been accepted. For A: In R, how do I apply regexes to specific parts of a string that contains a patte
Appreciated 11 weeks ago, created a post with more than 5 votes. For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Appreciated 3 months ago, created a post with more than 5 votes. For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Appreciated 3 months ago, created a post with more than 5 votes. For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Heat Map With Two Color Scales
Popular Question 3 months ago, created a question with more than 1,000 views. For Should We Have A Biostar Conference Or Meeting?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Why Don'T We Use Binary Format?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Why Don'T We Use Binary Format?
Scholar 4 months ago, created an answer that has been accepted. For A: mirDeep2 using bowtie vs. bwa - why do more aligned reads yield less miRNA
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Heat Map With Two Color Scales
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Heat Map With Two Color Scales
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Why Don'T We Use Binary Format?
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