User: Kevin Blighe

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. I currently work as freelance bioinformatician and Visiting Professor. I am also contracted to the European Commission for H2020 monitoring.

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'Incrocio le dita e spero'

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

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Developer / Maintainer of Bioconductor packages:

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

Posts by Kevin Blighe

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Comment: C: TCGA maf to vcf file conversion

... You will generate the FAM file on your own, by studying how it is structured: https://www.cog-genomics.org/plink/1.9/formats#fam ...

written 7 minutes ago by Kevin Blighe ♦ 46k

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Comment: C: Pipeline for SNP analysis

... > which pacakage we should use for SNP analysis in R? What do you mean? - you have not really explained what you want to do (?). So far, it seems that you just want to filter variants based on their frequencies in controls and patients. You should use other programs like ANNOVAR and Ensembl VEP ...

written 13 minutes ago by Kevin Blighe ♦ 46k

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Comment: C: awk extract certain line

... Okay, it is probably related to what Ram said, and something to do with the endline characters. ...

written 10 hours ago by Kevin Blighe ♦ 46k

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Comment: C: awk extract certain line

... Perhaps the tab-delimited part is not so key due to this section of your code `if($0~i)`, which ultimately searches for the pattern from file1 in the entire line ofrom file2 How did you copy the data from Excel to TXT? ...

written 11 hours ago by Kevin Blighe ♦ 46k

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Comment: C: awk extract certain line

... Your `awk` command works perfectly on my system (default Gawk). Your `grep` command returns nothing for me. I'm running Ubuntu 16.04 Be sure that your files are tab-delimited. Also, if you copied them from a Windows system, then they may have extraneous characters that can be removed with `dos2unix ...

written 11 hours ago by Kevin Blighe ♦ 46k

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Answer: A: Is there anyone who was a pure biologist?

... Before entering bioinformatics, I worked as: - Laboratory Technician in Dublin City Council (Ireland), testing wastewater, river, and lake samples for contamination as part of national and EU regulatory monitoring - Shellfish Microbiologist at Marine Institute Ireland, same as above but ...

written 18 hours ago by Kevin Blighe ♦ 46k

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Comment: C: How to analyze aCGH data in R?

... I'm not sure - I thought that *limma* had general functionality for Agilent arrays, though (both single and two-colour arrays). I wish that I had more time to check myself; otherwise, you can obtain the normalised data with the following code: library(Biobase) library(GEOquery) # l ...

written 22 hours ago by Kevin Blighe ♦ 46k

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Answer: A: TCGA maf to vcf file conversion

... To better help, you should show all commands that you have used. Some general advice: when converting a VCF to PLINK format, PLINK will ***not*** know what are the phenotypes. You need to create a custom FAM file that matches ***exactly*** to the order of samples in your PLINK object - you can then ...

written 22 hours ago by Kevin Blighe ♦ 46k

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Comment: C: Why does my TOM network heatmap for WGCNA display red background and golden modu

... Please Accept an answer (and up-vote it) if it has helped to solve the issue. ...

written 1 day ago by Kevin Blighe ♦ 46k

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Comment: C: Why AMOVA test is not active in Arlequin?

... Please take a look at the thread here: https://www.researchgate.net/post/Can_anyone_suggest_how_to_prepare_file_for_Arlequin_for_AMOVA ...

written 1 day ago by Kevin Blighe ♦ 46k

Latest awards to Kevin Blighe

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)

Good Answer 5 days ago, created an answer that was upvoted at least 5 times. For A: DESeq2 modelling and Wald's test

Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)

Good Answer 11 days ago, created an answer that was upvoted at least 5 times. For A: extract dendrogram cluster from pheatmap

Good Answer 11 days ago, created an answer that was upvoted at least 5 times. For A: DESeq2 modelling and Wald's test

Appreciated 11 days ago, created a post with more than 5 votes. For A: GSEA preranking metric for RNA Seq

Appreciated 11 days ago, created a post with more than 5 votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)

Appreciated 12 days ago, created a post with more than 5 votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)

Scholar 12 days ago, created an answer that has been accepted. For A: How to get data from GEO

Good Answer 12 days ago, created an answer that was upvoted at least 5 times. For A: DESeq2 modelling and Wald's test

Appreciated 12 days ago, created a post with more than 5 votes. For Why do PCA+tSNE/viSNE or PCA+UMAP, and not just tSNE/viSNE or UMAP on their own?

Appreciated 13 days ago, created a post with more than 5 votes. For Why do PCA+tSNE/viSNE or PCA+UMAP, and not just tSNE/viSNE or UMAP on their own?

Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)

Commentator 16 days ago, created a comment with at least 3 up-votes. For C: bash and awk code

Appreciated 16 days ago, created a post with more than 5 votes. For Why do PCA+tSNE/viSNE or PCA+UMAP, and not just tSNE/viSNE or UMAP on their own?

Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)

Good Answer 21 days ago, created an answer that was upvoted at least 5 times. For A: Batch effects : ComBat or removebatcheffects (limma package) ?

Appreciated 21 days ago, created a post with more than 5 votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)

Appreciated 22 days ago, created a post with more than 5 votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)

Teacher 25 days ago, created an answer with at least 3 up-votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)

Good Answer 25 days ago, created an answer that was upvoted at least 5 times. For A: Batch effects : ComBat or removebatcheffects (limma package) ?

Commentator 25 days ago, created a comment with at least 3 up-votes. For C: bash and awk code

Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)

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