Moderator: Kevin Blighe

gravatar for Kevin Blighe
Kevin Blighe21k
Reputation:
21,120
Status:
Trusted
Location:
University College London Cancer Institute
Website:
https://github.com/kev...
Last seen:
14 minutes ago
Joined:
9 months, 3 weeks ago
Email:
k**********@outlook.com

Irish bioinformatician and Senior Research Associate in Bioinformatics at University College London Cancer Institute.

Previously worked in USA, Italy, Malta, Brazil, UK, and Ireland.

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There are mountains in our way... but we climb a step every day...

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Nella fantasia, io vedo un mondo giusto; Lì, tutti vivono in pace e in onestà...
Io sogno d'anime che sono sempre libere

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Give me one moment in time, when I'm more than I thought I could be...

Posts by Kevin Blighe

<prev • 3,285 results • page 2 of 329 • next >
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Comment: C: How to manage self loops in gene coexpression network constructed from RNA-seq d
... Clustering algorithms will just cluster whatever data you provide. To remove self-loops, you can use the *NetworkAnalyzer* plugin for Cytoscape or just remove them in your correlation matrix after you generate it. For example, you could set all perfect correlations to NA or some low value, such tha ...
written 1 day ago by Kevin Blighe21k
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Comment: C: Stringtie output files
... I should additionally point out that *DDX11L1* is a pseudogene. So, it makes sense that it may have minimal expression if it has no promoter sequence or TSS such that transcription at a meaningful level could occur. ...
written 1 day ago by Kevin Blighe21k
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Comment: C: Converting UUID downloaded from GDC to TCGA names
... Try this: https://www.biostars.org/p/306400/#306517 ...
written 1 day ago by Kevin Blighe21k
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Comment: C: Issue using MaSuRCA-3.2.6
... Sorry, I am not sure what could be happening (and the question has gone unanswered on other sites, as you have seen). I actually used MaSuRCA 3.2.2 relatively recently (2017) and it worked fine, but on a much smaller bacterial genome. Here is my config file: ############################# # ...
written 1 day ago by Kevin Blighe21k
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Answer: A: Stringtie output files
... The one that was not included has coverage that falls below the threshold. It is virtually not expressed at all. Modify the `-C` and `-c` parameter to StringTie: > -C StringTie outputs a file with the given name with all transcripts in the provided reference file that are fully covered > by ...
written 1 day ago by Kevin Blighe21k
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Comment: C: Applying a function to a matrix
... Yes / Sim / Sea / Oui / Si ...
written 1 day ago by Kevin Blighe21k
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Comment: C: Applying a function to a matrix
... If they are the natural logged values, then, yes, just use either of: 2.71828182846^datamatrix exp(datamatrix) Then, they will be back on the scale they were before natural log transformation, i.e., anti natural log. Testing: 2.71828182846^log(2) [1] 2 exp(log(2)) ...
written 1 day ago by Kevin Blighe21k
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Answer: C: Applying a function to a matrix
... Wait, on which scale are your values currently? Already logged or not? You literally just want `e^value`? Then, that's just 2.71828182846^datamatrix ...or exp(datamatrix) ...
written 1 day ago by Kevin Blighe21k
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Comment: C: Issue using MaSuRCA-3.2.6
... So, it works now? ...
written 2 days ago by Kevin Blighe21k
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Comment: C: How to find p-value of the modules in WGCNA?
... But, if the blue module is not related to CaseControl, then what is your interpretation of that? It could represent the 'common' pathways across all of your samples. The interesting modules should be the ones that are statisatically significant to CaseControl. ...
written 2 days ago by Kevin Blighe21k

Latest awards to Kevin Blighe

Scholar 2 hours ago, created an answer that has been accepted. For A: Cuffcompare output: thousands of novel transcripts
Scholar 22 hours ago, created an answer that has been accepted. For A: Cuffcompare output: thousands of novel transcripts
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Cuffcompare output: thousands of novel transcripts
Scholar 1 day ago, created an answer that has been accepted. For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Good Answer 1 day ago, created an answer that was upvoted at least 5 times. For A: Complex Heatmap: Changing order of clusters
Commentator 3 days ago, created a comment with at least 3 up-votes. For C: DESEQ analysis contain rlog formation?
Scholar 4 days ago, created an answer that has been accepted. For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Appreciated 6 days ago, created a post with more than 5 votes. For Network plot from expression data in R using igraph
Commentator 6 days ago, created a comment with at least 3 up-votes. For C: bash and awk code
Appreciated 7 days ago, created a post with more than 5 votes. For Network plot from expression data in R using igraph
Scholar 7 days ago, created an answer that has been accepted. For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Scholar 7 days ago, created an answer that has been accepted. For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Scholar 11 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Appreciated 12 days ago, created a post with more than 5 votes. For Network plot from expression data in R using igraph
Scholar 12 days ago, created an answer that has been accepted. For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Appreciated 13 days ago, created a post with more than 5 votes. For Network plot from expression data in R using igraph
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Teacher 13 days ago, created an answer with at least 3 up-votes. For C: SNPs in 1000 genome project
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?

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