User: b.nota

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b.nota3.0k
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5 days, 19 hours ago
Joined:
1 year, 6 months ago
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Posts by b.nota

<prev • 511 results • page 1 of 52 • next >
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Comment: C: Selecting between p.value, FDR, Bonferroni
... I think factor is not the right term to use here, and is even confusing. In this case there are probably many regions (segments) either methylated or not. That is just one factor, but many tests. There for you'll have to use a multiple testing correction. ...
written 5 days ago by b.nota3.0k
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Comment: C: Selecting between p.value, FDR, Bonferroni
... For omics data most people use FDR corrected p-values, Bonferroni is much too stringent. Don't use raw p-values with omics data. ...
written 6 days ago by b.nota3.0k
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Comment: C: BWA: Why paired reads mapped to different chromosome?
... Biologically it could be explained by translocation, but if you have a lot reads it might be more likely to be caused by something technically. ...
written 6 days ago by b.nota3.0k
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Comment: C: Getting profit (plots, data) from my final GO enrichment analysis..
... If you do you enrichment in goseq, you can cluster GO terms (in heatmap) with [gogadget][1]. Or cluster them with cytoscape afterwards. [1]: https://www.biostars.org/p/206292/ ...
written 6 days ago by b.nota3.0k
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Comment: C: KEGG pathway and module enrichment for non-model fungi
... You can try goseq, if you have your KO-to-gene data in correct format. And yes, you'll have to use your whole assembly as a background. ...
written 6 days ago by b.nota3.0k
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Comment: C: Extract several fields from vcf file
... Have you tried AWK aleady? ...
written 6 days ago by b.nota3.0k
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Comment: C: how to retrieve protein sequences from enzyme/protein ids of kegg
... I think in R biomaRt you can retrieve protein sequences as well (never needed it before), did you look at biomaRt already? ...
written 7 days ago by b.nota3.0k
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Comment: C: RNA-seq batch effect correction
... Looks like I have seen this question before, deja vu. I still think with such a poor design there is no statistical sound method to get something out of this data set. Try to redo the experiment where at least before and after are in the same batch... ...
written 7 days ago by b.nota3.0k
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Comment: C: Postdoc in Machine Learning Methods for Single-Cell Data
... There is an email address and a phone number, show some assertiveness I would suggest ;-) ...
written 7 days ago by b.nota3.0k
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Comment: A: Explanation of ENSEMBL GTF features
... Thanks guys for your input. maybe I should have said that I have a PhD in genetics/genomics and work as a bioinformatician for years already. Seen by the answers, that was probably not clear. This wasn't a newbie question about how simple genetics works, but I couldn't find the definition/criteria ...
written 11 days ago by b.nota3.0k

Latest awards to b.nota

Commentator 6 days ago, created a comment with at least 3 up-votes. For C: RNA to protein in bash?
Popular Question 27 days ago, created a question with more than 1,000 views. For Find genes of enriched known motif results in HOMER
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Find genes of enriched known motif results in HOMER
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Scholar 5 months ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Blasting against multiple fasta file
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Appreciated 6 months ago, created a post with more than 5 votes. For A: Bioinformatics freelancers needed
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Blasting against multiple fasta file
Scholar 8 months ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
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Scholar 8 months ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
Appreciated 9 months ago, created a post with more than 5 votes. For A: Bioinformatics freelancers needed
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Blasting against multiple fasta file
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