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User: Kevin Blighe

gravatar for Kevin Blighe
Kevin Blighe • 1.3k
Reputation:
1,270
Status:
Trusted
Location:
Republic of Ireland
Website:
https://github.com/kev...
Last seen:
2 hours ago
Joined:
3 weeks, 4 days ago
Email:
k**********@outlook.com

Professional experience:

  • Harvard Medical School, Boston, USA (Fellow in Medicine)
  • Queen Mary University of London, London, UK (Senior Bioinformatician)
  • Imperial College London, London, UK (Bioinformatician)
  • Ospedale Maggiore Policlinico, Milan, Italy (Bioinformatics Analyst)
  • NHS England, Sheffield, UK (Lead Bioinformatician)

Education:

  • Ph.D. in Breast Cancer cfDNA, University of Leicester, Leicester, UK
  • B.Sc. (Hons.) in Industrial Biology, Institute of Technology Carlow, Ireland
  • B.Sc. (Hons.) in Computer Science, Dublin Institute of Technology, Dublin, Ireland
  • Christian Brothers School, Naas, Ireland

Posts by Kevin Blighe

<prev • 269 results • page 1 of 27 • next >
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Comment: C: Where can I find DNase-seq assays of cell line MCF-10A?
... Have you tried searching the Sequence Read Aechive? - https://www.ncbi.nlm.nih.gov/sra ...
written 4 hours ago by Kevin Blighe • 1.3k
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Comment: C: How to cluster the upregulated and downregulated genes in heatmap?
... Looks great! Yes, labeling is a major issue, but there are different ways of tackling it: #Modify `cexRow` and change the dimensions of the heatmap `cexRow` controls the size of the labels, as you probably know, whilst modifying the dimensions of the heatmap could work whereby you elongate the hea ...
written 4 hours ago by Kevin Blighe • 1.3k
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Answer: A: Cufflinks analysis of Tophat BAM file
... Your RAM and I/O are being used more efficiently when you split the file. ...
written 9 hours ago by Kevin Blighe • 1.3k
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Answer: A: Working with Differentially Methylated Regions(DMRs)
... I also recently analysed methylation data from the TCGA and I just applied a Wilcoxon Signed Rank Test (in R) to each probe, adjusting P values by FDR. I also calculated the difference in mean β value between the probe in tumours and normals. A statistically significant probe was then defined as on ...
written 9 hours ago by Kevin Blighe • 1.3k
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Answer: A: How to get CDE ID corresponds to each column feature of clinical data from TCGA
... Dear Fdota, I have just responded to your other thread, effectively answering this question: https://www.biostars.org/p/274391/#274521 Kevin ...
written 9 hours ago by Kevin Blighe • 1.3k
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Comment: C: TCGA clinical feature meaning of "pct_tumor_invasion" for TCGA-UCEC project (Ute
... No problem! I have never used TCGAbiolinks as I normally download the data myself from the GDC Data Portal using manifest files. However, the TCGA being the TCGA, they have lots of data to manage and are constantly re-organising the data. The original files that I downloaded are now in the GDC Legac ...
written 9 hours ago by Kevin Blighe • 1.3k
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Comment: C: How to cluster the upregulated and downregulated genes in heatmap?
... Great - let me know how it goes! ...
written 11 hours ago by Kevin Blighe • 1.3k
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Answer: A: Using Plink, get allele frequencies for a subset of individuals
... My guess is an encoding issue with your hyphens. PLINK may have converted these to something else when you read your data into PLINK initially - have you checked the sample names as they appear in PLINK? Also check the formatting of the hyphen in your */path/cases.txt* file. There are different enc ...
written 11 hours ago by Kevin Blighe • 1.3k
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Answer: A: How to cluster the upregulated and downregulated genes in heatmap?
... You can try messing around with different combinations of the distance, linkage, and re-order functions. With the `heatmap.2` function (assuming that you're using `heatmap.2`), you can specify the following as parameters: #Re-order rows/columns by mean, use 1-Pearson's correlation distance, and ...
written 11 hours ago by Kevin Blighe • 1.3k
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Answer: A: TCGA clinical feature meaning of "pct_tumor_invasion" for TCGA-UCEC project (Ute
... If you want to search for one of those terms used by the TCGA, you should go by the CDE code assigned to each term, which should be listed in the third row of the clinical data that you downloaded. For pct_tumor_invasion in the endometrial cancer dataset that I have, the CDE ID is CDE ID 3104403. H ...
written 13 hours ago by Kevin Blighe • 1.3k

Latest awards to Kevin Blighe

Scholar 8 hours ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Scholar 11 hours ago, created an answer that has been accepted. 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
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Scholar 5 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
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Scholar 7 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Compare two columns of same file as paired rows
Scholar 8 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
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Scholar 13 days ago, created an answer that has been accepted. For A: ChIP-Seq identification of peaks
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Scholar 15 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
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