Moderator: Kevin Blighe

gravatar for Kevin Blighe
Kevin Blighe51k
Reputation:
51,020
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Website:
https://github.com/kev...
Twitter:
@biostar41557
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Google Scholar Page
Last seen:
an hour ago
Joined:
2 years, 2 months ago
Email:
k****@clinicalbioinformatics.co.uk

From The Emerald Isle. I have worked in bioinformatics as postdoc and freelance consultant in Europe, USA, and South America, both in academia and private industry, and also in clinical genetics / health services.

Developer / Maintainer of Bioconductor packages:

LinkedIn: https://www.linkedin.com/in/clinicalbioinformatics/

 

Posts by Kevin Blighe

<prev • 7,089 results • page 1 of 709 • next >
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Comment: A: GWAS result display
... A barplot (ordered or un-ordered) of the beta coefficients? ...
written 10 hours ago by Kevin Blighe51k
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Answer: A: Copy number profile using Control-FREEC
... As you have used *_ratio.txt*, each dot represents the predicted copy number for each window. The size of the window will depend on your input configuration file. Kevin ...
written 10 hours ago by Kevin Blighe51k
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Comment: C: Normal sample from GDC
... It is available for me. Which error message are you receiving? ...
written 10 hours ago by Kevin Blighe51k
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Answer: A: GWAS - QC & Tutorials.
... My own selection / collection: Quality Control ------- - Quality control procedures for genome-wide association studies - Data quality control in genetic case-control association studies (credit: alessandrotestori7) General GWAS / genetic studies -------------- - A comprehensive re ...
written 19 hours ago by Kevin Blighe51k
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Comment: C: RNAseq read counts generated by FeatureCounts
... Cross-posted: https://support.bioconductor.org/p/126561/ ...
written 20 hours ago by Kevin Blighe51k
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Answer: A: Normal sample from GDC
... You can infer tumour and normal samples via the TCGA barcode: https://www.biostars.org/p/313063/#313066 Kevin ...
written 1 day ago by Kevin Blighe51k
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Answer: A: How to get gene name for SNPs RS ids
... Yet another answer, via *biomaRt*, in R: https://www.biostars.org/p/336724/#336731 Kevin ...
written 1 day ago by Kevin Blighe51k
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Comment: C: Why is the number of genes in certain a module in WGCNA super high?
... Not much to add, really, except that I would not permit that WGCNA's results dictate your conclusions for your work. It may make sense, given your experiment, to have roughly half of the protein coding transcriptome appearing in one module like that - I'm not sure. ...
written 1 day ago by Kevin Blighe51k
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Comment: C: haploview to cervus
... Ah, they may mean the GEN ('Oxford') format, which is outlined here on PLINK2's website: https://www.cog-genomics.org/plink/1.9/formats#gen I cannot exactly recall the HaploView format but I believe it is similar. Unfortunately, for whatever reason when all of these genetics analysis programs were ...
written 1 day ago by Kevin Blighe51k
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Comment: C: problem for Collapsing Probes For Same Gene in microarray gene expression data
... I am not to know the source of that particular problem. Please review all steps of your code, reviewing both input and output, in order to understand why there may be no gene name there. ...
written 1 day ago by Kevin Blighe51k

Latest awards to Kevin Blighe

Good Answer 7 hours ago, created an answer that was upvoted at least 5 times. For A: PCA plot from read count matrix from RNA-Seq
Appreciated 7 hours ago, created a post with more than 5 votes. For PCAtools: everything Principal Components Analysis
Teacher 8 hours ago, created an answer with at least 3 up-votes. For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Good Answer 3 days ago, created an answer that was upvoted at least 5 times. For A: PCA plot from read count matrix from RNA-Seq
Appreciated 3 days ago, created a post with more than 5 votes. For PCAtools: everything Principal Components Analysis
Popular Question 3 days ago, created a question with more than 1,000 views. For Parallel processing in R
Scholar 5 days ago, created an answer that has been accepted. For A: Help finding specific breast cancer datasets
Appreciated 8 days ago, created a post with more than 5 votes. For Parallel processing in R
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Gold Standard 9 days ago, created a post with more than 25 bookmarks. For A: PCA plot from read count matrix from RNA-Seq
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Scholar 10 days ago, created an answer that has been accepted. For A: Help finding specific breast cancer datasets
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Appreciated 10 days ago, created a post with more than 5 votes. For Parallel processing in R
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Scholar 12 days ago, created an answer that has been accepted. For A: Help finding specific breast cancer datasets
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Help finding specific breast cancer datasets
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Appreciated 13 days ago, created a post with more than 5 votes. For Parallel processing in R
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: Help finding specific breast cancer datasets
Scholar 16 days ago, created an answer that has been accepted. For A: Help finding specific breast cancer datasets
Great Question 16 days ago, created a question with more than 5,000 views. For Network plot from expression data in R using igraph
Good Answer 17 days ago, created an answer that was upvoted at least 5 times. For A: Can I use TCGA FPKM-UQ values directly to compare across samples without any pre
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: Help finding specific breast cancer datasets
Scholar 19 days ago, created an answer that has been accepted. For A: Help finding specific breast cancer datasets

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