Moderator: Kevin Blighe

gravatar for Kevin Blighe
Kevin Blighe45k
Reputation:
45,440
Status:
Trusted
Location:
Website:
https://github.com/kev...
Twitter:
BiostarsRus
Scholar ID:
Google Scholar Page
Last seen:
3 hours ago
Joined:
1 year, 10 months ago
Email:
k****@clinicalbioinformatics.co.uk

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.

----------------------------------------------

'Incrocio le dita e spero'

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

----------------------------------------------

Developer / Maintainer of Bioconductor packages:

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

 

Posts by Kevin Blighe

<prev • 6,461 results • page 2 of 647 • next >
0
votes
0
answers
78
views
0
answers
Comment: C: Calculate disease risk based on the genoytype of some SNPs
... 'polygenic risk score' is actually just a generic term, and there are many ways to generate a 'risk score' from multiple genotypes. The algorithms that I have seen (and including my own algorithm) start with the beta coefficients, which are obtained once you fit a regression model to your data. As y ...
written 23 hours ago by Kevin Blighe45k
0
votes
0
answers
52
views
0
answers
Comment: C: Correcting batch effect in unevenly distributed groups
... Hola Jenn, how can you define 'not succeeding' [with limma]? Can you show the PCA bi-plot with percent variation explained for each PC? Why are you using limma if this is RNA-seq - I assume limmas / voom? > I have two main questions, first, can I find a vector/value/something > using samples ...
written 1 day ago by Kevin Blighe45k
0
votes
1
answer
66
views
1
answers
Answer: A: Merge DEseq and Cufflinks outputs
... If you just want to use the test statistics (p-values, fold-changes, etc) from Cufflinks and DESeq2, then I would aim to perform what is called a 'meta analysis'. Otherwise, I would retrieve the raw data (FASTQ or BAM) from both experiments and re-process everything myself using the same pipeline. ...
written 1 day ago by Kevin Blighe45k
0
votes
0
answers
47
views
0
answers
Comment: C: Bifurcate network between genes and pathways
... Until you provide more information, this thread will remain closed. We cannot be expected to answer questions like this that are severely lacking in details and effort. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help wi ...
written 1 day ago by Kevin Blighe45k
1
vote
1
answer
114
views
1
answers
Answer: A: Differential network analysis for two treatments
... Jon, your post is severely lacking in details. As an example, you have not stated whether or not your data is normalised. How can we help if no information is provided? Anyway, as per Lila, if you follow the DESeq2 vignette (see the link in Lila's answer), then you will learn a lot about how you ca ...
written 1 day ago by Kevin Blighe45k
0
votes
0
answers
52
views
0
answers
Comment: C: Too many fails converting gene SYMBOL to ENTREZID
... Your code is not reproducible because `diff_expr_tenmg` was never instantiated (?). Have you triied biomaRt to convert the gene symbols? ...
written 1 day ago by Kevin Blighe45k
0
votes
1
answer
48
views
1
answers
Answer: A: FANTOM5 enhancers: intepretations
... You can assume that the enhancer region is defined by the first 3 columns. I assume that 'TCs' refers to 'tag clusters'; so, the higher the number, the greater the activity of the enhancer region. By the way, FANTOM6 is coming out: https://www.biorxiv.org/content/10.1101/700864v2 Kevin ...
written 1 day ago by Kevin Blighe45k
0
votes
0
answers
78
views
0
answers
Comment: C: Calculate disease risk based on the genoytype of some SNPs
... You clearly state that you are a beginner, but the project that you are aiming to do is somewhat advanced, at least from my perspective. Are you at least familiar with regression analysis, and know how to conduct this in the context of genetic variants? What data do you currently have (paste an exam ...
written 1 day ago by Kevin Blighe45k
0
votes
0
answers
50
views
0
answers
Comment: C: CNV analysis for tumor panel
... There are many dozens of copy number calling programs. FREEC and XHMM are actually regarded as among the best. What, exactly, is your input data? - genome sequencing, exome / targeted sequencing, microarray, or PCR? ...
written 1 day ago by Kevin Blighe45k
1
vote
0
answers
67
views
0
answers
Comment: C: The Cancer Genome Atlas (TCGA) gene expression analysis
... I have not used the data from Broad Firehose; however, UCSC's Xena Browser has expression data available in HTseq and FPKM counts: https://xenabrowser.net/datapages/ (look for the 'GDC TCGA' datasets) You will want those HTseq counts, however, you will have to convert them back to raw integer count ...
written 2 days ago by Kevin Blighe45k

Latest awards to Kevin Blighe

Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
Scholar 1 day ago, created an answer that has been accepted. For A: How to get data from GEO
Appreciated 3 days ago, created a post with more than 5 votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Help finding specific breast cancer datasets
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
Scholar 5 days ago, created an answer that has been accepted. For A: How to get data from GEO
Good Answer 6 days ago, created an answer that was upvoted at least 5 times. For A: Batch effects : ComBat or removebatcheffects (limma package) ?
Scholar 8 days ago, created an answer that has been accepted. For A: Help finding specific breast cancer datasets
Scholar 8 days ago, created an answer that has been accepted. For A: How to get data from GEO
Appreciated 9 days ago, created a post with more than 5 votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
Teacher 10 days ago, created an answer with at least 3 up-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
Gold Standard 14 days ago, created a post with more than 25 bookmarks. For Network plot from expression data in R using igraph
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
Appreciated 17 days ago, created a post with more than 5 votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
Commentator 22 days ago, created a comment with at least 3 up-votes. For C: bash and awk code
Commentator 23 days ago, created a comment with at least 3 up-votes. For C: bash and awk code
Appreciated 26 days ago, created a post with more than 5 votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
Appreciated 26 days ago, created a post with more than 5 votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Help finding specific breast cancer datasets
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
Commentator 28 days ago, created a comment with at least 3 up-votes. For C: bash and awk code
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1494 users visited in the last hour