Moderator: Kevin Blighe

gravatar for Kevin Blighe
Kevin Blighe16k
Reputation:
16,450
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Trusted
Location:
University College London Cancer Institute
Website:
https://github.com/kev...
Last seen:
5 hours ago
Joined:
7 months, 3 weeks ago
Email:
k**********@outlook.com

...facing difficulty? - everything will be alright!

 

There are mountains in our way... but we climb a step everyday...

 

I am Senior Research Associate in Bioinformatics at University College London. I previously worked in USA, Italy, Malta, Brazil, UK, and Ireland.

Posts by Kevin Blighe

<prev • 2,561 results • page 1 of 257 • next >
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Answer: A: hierarchical cluster of drug treatment after correlation analysis
... Check the distribution of your data first by generating a histogram. If it looks like that typical 'bell' curve (binomial distribution), then use *Euclidean* distance. If not, then you may consider correlation dissimilarities via 1 minus Spearman correlation. You could also transform your data to t ...
written 7 hours ago by Kevin Blighe16k
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Answer: A: SNP dataset and Z Score
... Your questions are not a nuisance, so, do not feel bad for asking. In association studies, the usual focus at each SNP position is the minor allele, i.e., the SNP allele that has the lowest frequency in the samples being studied in your dataset - I am assuming that you know this? At some genotyped ...
written 7 hours ago by Kevin Blighe16k
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Comment: C: How to calculate distribution of mapped read over classes of RNA?
... By default, I believe featureCounts does not count multi-mapped reads. ...
written 10 hours ago by Kevin Blighe16k
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Comment: C: fantom5 enhancers GRCh38
... From where did you obtain the data? ...
written 20 hours ago by Kevin Blighe16k
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Comment: C: Genome-wide CRISPR/Cas9 and gene expression?
... I am not aware but it would be great to do that via whole genome phased sequencing and then RNA-seq. Indirectly, the information may already exist, as, if you excise a disease allele, you may be restoring the wild-type state, and, thus, the affected gene and pathways could return to their normal sta ...
written 20 hours ago by Kevin Blighe16k
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Comment: C: Human genes correlation to Bacterial genes
... When you correlate, you have to have the same number observations in the vectors that you are correlating. You cannot just randomly correlate any data-matrices. The only way that you can do this is by correlating each row of *Human* with each row of *Bacteria*, but then you only have 3 observations ...
written 20 hours ago by Kevin Blighe16k
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Comment: C: qqplot for the P-values dervided from permutation test in Plink
... To help to understand that, you may want to take a look at this Stats StakOverflow answer: https://stats.stackexchange.com/questions/101274/how-to-interpret-a-qq-plot - Above the expected distribution implies that the data is more 'spread' (dispersed) than expected. - Below the expected distri ...
written 1 day ago by Kevin Blighe16k
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Comment: C: Protocol To Downlad TCGA Data From GDC
... Thanks Sean - that's what I expected. We are currently awaiting dbGaP approval (not my current institute). ...
written 1 day ago by Kevin Blighe16k
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Answer: A: How to calculate distribution of mapped read over classes of RNA?
... There are a few ways to do this, but first you should download the GENCODE '***Comprehensive gene annotation***' reference transcriptome file for either GRCh38 / hg38 or GRCh37 / hg19. Obviously, the version will depend on the reference genome build to which you have aligned your reads. - GRCh38 / ...
written 1 day ago by Kevin Blighe16k
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Answer: A: RNAseq sva-seq drops number of DE genes?
... Hello, My own take on this: do not do any adjustments using SVA-seq unless you are certain that there are effects in the data that are not related to biological effects and that are unidentified, i.e., do not use SVA-seq just for the sake of it or because someone said that you have to use it. By us ...
written 1 day ago by Kevin Blighe16k

Latest awards to Kevin Blighe

Scholar 10 hours ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Scholar 1 day ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
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: 012 genotype matrix using vcf tools (converting rows to columns)
Teacher 2 days ago, created an answer with at least 3 up-votes. 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
Appreciated 2 days ago, created a post with more than 5 votes. For Network plot from expression data in R using igraph
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 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
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: How to match genes of one file to another but in multiple columns
Scholar 3 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: 012 genotype matrix using vcf tools (converting rows to columns)
Teacher 4 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
Scholar 4 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Appreciated 4 days ago, created a post with more than 5 votes. For Network plot from expression data in R using igraph
Scholar 6 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Scholar 6 days ago, created an answer that has been accepted. For A: 012 genotype matrix using vcf tools (converting rows to columns)
Teacher 8 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: 012 genotype matrix using vcf tools (converting rows to columns)
Scholar 9 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 10 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: Compare two columns of same file as paired rows

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