Moderator: Kevin Blighe

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Kevin Blighe6.5k
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Location:
Republic of Ireland (Éire)
Website:
https://github.com/kev...
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Joined:
2 months, 2 weeks ago
Email:
k**********@outlook.com

Thinking outside that box...

  • Postdocs in asthma (Boston); breast cancer and leukaemia (London); rheumatoid arthritis (London).
  • Clinical genetics exp. in Sheffield Children's Hospital (Sheffield); Ospedale Maggiore Policlinico (Milan)
  • PhD in breast cancer circulating free DNA (Leicester)
  • Undergraduates in Computer Science (Dublin); Industrial Biology (Carlow)

Blighe K, 2010 - excerpts from 'Our Love Is Art'
The roses dance the melodies of the breeze, in a perpetual embrace amidst plants and trees.

Their portrait could be painted as indescribable perfection, but already it exists, in your reflection.

You are the roses of my world, You seed life to what is best in me.

Each time you paint a part of our masterpiece, Our love melts further, into destiny.

Posts by Kevin Blighe

<prev • 1,059 results • page 1 of 106 • next >
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Comment: C: Paralellize samtools piped with awk
... An expansion to Michael's script idea, you should do something like this: ls 4*.bam | while read BAM do [parallelised code executed on "${BAM}"] done Alternatively, you could split the output of ls into chunks and then run each in separate terminals: ls 4*.bam | split --lin ...
written 53 minutes ago by Kevin Blighe6.5k
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Comment: C: Fasted method to genotype given SNPs from NGS data
... If you are just interested in identifying single base changes, then samtools mpileup / bcftools call is much quicker than the GATK, and has greater sensitivity for single nucleotide changes (from my experience). Take a look at the code that I post here: https://www.biostars.org/p/284097/#284299 Al ...
written 1 hour ago by Kevin Blighe6.5k
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Comment: C: Heatmap based with FPKM values
... DiffExpressedGenes is a vector that contains the name of all of your differentially expressed genes. These names should all be part of the rownames of your FPKM matrix. I beiieve that you can include FPKM values that are 0. Why? - due to the fact that we scale / transform the data to the Z-scale, t ...
written 1 hour ago by Kevin Blighe6.5k
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Answer: A: Heatmap based with FPKM values
... Yes, you can begin with FPKM values but you will have to transform these values and also filter the dataset with your 800 differentially expressed genes. On that note, 800 is a lot of genes. Try to increase your cut-offs of statisticaly significntly differentially expressed. Try things like: - FDR ...
written 10 hours ago by Kevin Blighe6.5k
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Comment: C: Does anyone has van't Veer et al. (2002) breast cancer data set?
... I think that it is indeed the column #3 ('*series*') in the pData that is the key. I just found this comment by someone who worked on it (I assume): > Benjamin Haibe-Kains: It was a complicated process of curation and > unfortunately we did not keep track of all the changes. However, you > ...
written 11 hours ago by Kevin Blighe6.5k
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Comment: C: Does anyone has van't Veer et al. (2002) breast cancer data set?
... I think that it can be explained by the fact that the dataset include patients from 2 studies, some of which may have been used in both [studies]. It's just not clear, though. On their Bioconductor page, they state that the Van de Vijver dataset was **[edit:] 117** patients, which I found through t ...
written 11 hours ago by Kevin Blighe6.5k
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Comment: C: Does anyone has van't Veer et al. (2002) breast cancer data set?
... This issue appears to go all the way back to 2012 and was never fixed: https://github.com/ramhiser/datamicroarray/issues/5 You may also want to follow-up on GitHub. ...
written 12 hours ago by Kevin Blighe6.5k
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Answer: A: GDC API query to map HT-seq FPKM UUID to a Case UUID
... Hello, With the TCGA data, it can indeed be difficult to just figure out which sample is which. A lot of time and effort has to be invested just to organise the data for a particular project. Here's how I did it for a recent TCGA dataset that I re-analysed: In order to search for the Case UUID fro ...
written 12 hours ago by Kevin Blighe6.5k
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Comment: C: Preprocess QCs in metabolomics workflow together with samples - yes or no?
... Well, we should use the word 'solved' very lightly! With metabolomics, I think that it's open game with regard to how the data is processed. Your logic does make sense, i.e., yo go back and re-perform the pre-processing step with just the cases/controls (and after they've been filtered). ...
written 12 hours ago by Kevin Blighe6.5k
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Comment: C: how to get genes and their interactions from RNA-Seq data?
... If you are looking to model or 'map' your RNA-seq data to current known and curated interaction networks ('pathways'), then just do simple pathway analysis with DAVID or some of the other tools mentioned here. There are also commercial tools. You only now mention SRA (not in your original question) ...
written 12 hours ago by Kevin Blighe6.5k

Latest awards to Kevin Blighe

Good Answer 1 day ago, created an answer that was upvoted at least 5 times. For A: build the expression matrix step by step from GEO raw data
Appreciated 1 day ago, created a post with more than 5 votes. For A: Visualization for ChIP-seq analysis
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Compare two columns of same file as paired rows
Appreciated 2 days ago, created a post with more than 5 votes. For A: Visualization for ChIP-seq analysis
Scholar 2 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Compare two columns of same file as paired rows
Scholar 4 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Compare two columns of same file as paired rows
Oracle 4 days ago, created more than 1,000 posts (questions + answers + comments).
Scholar 5 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Appreciated 5 days ago, created a post with more than 5 votes. For A: Visualization for ChIP-seq analysis
Scholar 5 days ago, created an answer that has been accepted. For A: ChIP-Seq identification of peaks
Good Answer 5 days ago, created an answer that was upvoted at least 5 times. For A: Visualization for ChIP-seq analysis
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Compare two columns of same file as paired rows
Scholar 5 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Compare two columns of same file as paired rows
Scholar 6 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Compare two columns of same file as paired rows
Scholar 9 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Good Answer 10 days ago, created an answer that was upvoted at least 5 times. For A: Visualization for ChIP-seq analysis
Appreciated 10 days ago, created a post with more than 5 votes. For A: Visualization for ChIP-seq analysis
Good Answer 10 days ago, created an answer that was upvoted at least 5 times. For A: build the expression matrix step by step from GEO raw data
Scholar 10 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Compare two columns of same file as paired rows
Scholar 11 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows

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