Moderator: Kevin Blighe

gravatar for Kevin Blighe
Kevin Blighe55k
Reputation:
54,740
Status:
Trusted
Location:
Porto Alegre / London
Website:
https://github.com/kev...
Twitter:
KevinBlighe
Scholar ID:
Google Scholar Page
Last seen:
6 minutes ago
Joined:
2 years, 6 months ago
Email:
k****@clinicalbioinformatics.co.uk

 

From The Emerald Isle.

Developer / Maintainer of Bioconductor packages:

Other packages:

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

 

Posts by Kevin Blighe

<prev • 7,476 results • page 2 of 748 • next >
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Comment: C: How to get read counts on transcript level using featurecounts?
... Hey Lior, what is the 'ground truth'? ...
written 1 day ago by Kevin Blighe55k
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Answer: A: tool for the new protocol of WES for CNV detection
... There are countless CNV detection programs out there, but two that I, personally, hold in high regard are Control FREEC and HMMcopy. Kevin ...
written 1 day ago by Kevin Blighe55k
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Comment: C: calculate Per variant Heterozygosity from VCF file
... Thank you. Can you show some sample output just to help users? ...
written 1 day ago by Kevin Blighe55k
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Comment: C: How to log-transform OR and its SE in GWAS summary statistics
... How was your data produced, and what is your next intended step for the analysis? Ultimately, why do you feel that you need to log transform these? ...
written 1 day ago by Kevin Blighe55k
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Answer: A: Question regarding journal publications
... *Bioinformatics* journal is free, but there are restrictions about what qualifies for a free publication with this journal. Most likely it is not suited to general research. ...
written 1 day ago by Kevin Blighe55k
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Comment: C: Obtaining P Values from Cox Regression in R
... Hello Professor Menon, that is due to the fact that your `res` object is not produced directly from `coxph()`. You will have to apply `summary()` to your `models` list object, most likely via another lapply function. Something like I do in this code chunk from my package *RegParallel*: - https:// ...
written 1 day ago by Kevin Blighe55k
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Answer: A: Obtaining P Values from Cox Regression in R
... The p-values can be obtained via the `summary()` function applied to your model. The summary function will then have the following values of interest - `coefficients`, coefficient p-values, SEs, beta coefficients, etc. - `logtest`, likelihood ratio test p-value - `sctest`, Score / logRank test ...
written 2 days ago by Kevin Blighe55k
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Comment: C: RNAseq cell line as a covariate
... Meta-analysis is not quite my area but the program that comes to mind is *rankProd* (in R). I don't know which specific method(s) is / are implemented in *rankProd*, though. I cannot really comment on the mutation part. It seems like it is only relevant to one cell-line. If you are interested in pe ...
written 2 days ago by Kevin Blighe55k
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Comment: C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab
... Hey, sure thing and no problem, you just need to use: lab = NA ...
written 2 days ago by Kevin Blighe55k
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Comment: C: PCA plot color differentiation
... Is the `Reds` or `Greens` palette sufficient? Alternatively, you can literally use any colours that you want, like this: myPalette <- c('white','pink','red2','red4') colorRampPalette(myPalette)(length(unique(x)))[factor(x, levels = c('01', '03', '05', '08'))] ...
written 2 days ago by Kevin Blighe55k

Latest awards to Kevin Blighe

Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Scholar 2 days ago, created an answer that has been accepted. For A: R package ArrayExpress error
Good Answer 3 days ago, created an answer that was upvoted at least 5 times. For A: Alternate nucleotide is more frequent than reference nucleotide. OMG I'm dizzy.
Scholar 5 days ago, created an answer that has been accepted. For A: R package ArrayExpress error
Scholar 5 days ago, created an answer that has been accepted. For A: R package ArrayExpress error
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Good Answer 13 days ago, created an answer that was upvoted at least 5 times. For A: Alternate nucleotide is more frequent than reference nucleotide. OMG I'm dizzy.
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Scholar 18 days ago, created an answer that has been accepted. For A: R package ArrayExpress error
Appreciated 21 days ago, created a post with more than 5 votes. For Determine % of reference genome covered by aligned SAM/BAM
Scholar 25 days ago, created an answer that has been accepted. For A: R package ArrayExpress error
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Scholar 26 days ago, created an answer that has been accepted. For A: R package ArrayExpress error
Scholar 26 days ago, created an answer that has been accepted. For A: R package ArrayExpress error
Commentator 28 days ago, created a comment with at least 3 up-votes. For C: bash and awk code
Scholar 4 weeks ago, created an answer that has been accepted. For A: R package ArrayExpress error
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Building a predictive model by a list of genes
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Automatic Outlier Detection for RNA-seq data
Appreciated 4 weeks ago, created a post with more than 5 votes. For PCAtools: everything Principal Components Analysis
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Scholar 4 weeks ago, created an answer that has been accepted. For A: R package ArrayExpress error
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Automatic Outlier Detection for RNA-seq data
Appreciated 5 weeks ago, created a post with more than 5 votes. For PCAtools: everything Principal Components Analysis

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