Moderator: Kevin Blighe

gravatar for Kevin Blighe
Kevin Blighe41k
Reputation:
40,890
Status:
Trusted
Location:
Guy's Hospital, London
Website:
https://github.com/kev...
Twitter:
KevinBlighe
Scholar ID:
Google Scholar Page
Last seen:
an hour ago
Joined:
1 year, 7 months ago
Email:
k****@clinicalbioinformatics.co.uk

Do not worry... I am Irish.

'Incrocio le dita e spero'

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

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

Developer / Maintainer of Bioconductor packages:

Posts by Kevin Blighe

<prev • 5,939 results • page 1 of 594 • next >
0
votes
0
answers
21
views
0
answers
Comment: C: Convert gff.gz file to gtf
... gunzip GCF_000697945.2_Focc_2.1_genomic.gff.gz ...
written 1 hour ago by Kevin Blighe41k
0
votes
1
answer
57
views
1
answers
Answer: A: Question about chromosomal instability
... > Can anyone help me out how to check the chromosomal instability of a > particular gene. This statement does not make sense due to the fact that *chromosomal instability* is a general term that has no defined criteria. A gene may exhibit deletion or some other copy number or structural vari ...
written 11 hours ago by Kevin Blighe41k
0
votes
1
answer
61
views
1
answers
Answer: A: limma, best practices review paper?
... I cannot define the word "*better*", but Limma is to microarray analyses what PLINK is to GWAS association testing. It became the leading microarray differential expression analysis tool long ago and has much general functionality for microarray data processing, too. The package is downloaded >10 ...
written 11 hours ago by Kevin Blighe41k
0
votes
2
answers
132
views
2
answers
Comment: C: PCA analysis with R
... One can infer that it uses `prcomp()` based on my example above, yes. However, the functionality of the program should be improved as it leaves much room for doubt. ...
written 11 hours ago by Kevin Blighe41k
0
votes
2
answers
132
views
2
answers
Comment: C: PCA analysis with R
... Yes, I literally had to run the code myself to find out... something did not seem correct! ...
written 14 hours ago by Kevin Blighe41k
3
votes
2
answers
132
views
2
answers
Answer: A: PCA analysis with R
... The PCA function that it uses is `prcomp()`, which is the same as what my own package (PCAtools) and DESeq2 use. Yes, it is performing partitioning around medoids (PAM) and identifying X number of clusters (user pre-selects desired number as second parameter to `pam()`). `autoplot()` then performs ...
written 16 hours ago by Kevin Blighe41k
0
votes
0
answers
62
views
0
answers
Comment: C: Interested in Machine Learning?
... On the website, it says that the deadline is 14th May, not 4th May as indicated in the poster (above). Which is it? ...
written 16 hours ago by Kevin Blighe41k
0
votes
1
answer
99
views
1
answers
Comment: C: How to extract entire info column from VCF file using bcftools
... Indeed, and, with `cut` or `awk`, you can still merge these via `paste` to output of `bcftools query`, which is still very useful to use to extract tag information that is embedded in INFO or FORMAT: paste \ <(bcftools view test.bcf | \ awk '!/^#/ {print $1":"$2":"$4":"$5}') \ ...
written 16 hours ago by Kevin Blighe41k
1
vote
0
answers
123
views
0
answers
Comment: C: RNA Seq analysis of rice samples
... Cool - that seems like the problem (multi-mapped reads), as you imply. ...
written 16 hours ago by Kevin Blighe41k
1
vote
1
answer
1.0k
views
1
answers
Comment: C: How to calculate moderated z-score (MODZ)
... I have moved it to a comment. If you provide an answer, please answer the question that was originally asked. ...
written 1 day ago by Kevin Blighe41k

Latest awards to Kevin Blighe

Teacher 14 hours ago, created an answer with at least 3 up-votes. For A: Annotate Affymetrix probesets to Gene symbols
Epic Question 3 days ago, created a question with more than 10,000 views. For Network plot from expression data in R using igraph
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Annotate Affymetrix probesets to Gene symbols
Good Answer 7 days ago, created an answer that was upvoted at least 5 times. For A: How to exclude some of breast cancer subtypes just by looking at gene expressio
Teacher 12 days ago, created an answer with at least 3 up-votes. For C: TCGA immunotherapy treated melanoma data
Commentator 12 days ago, created a comment with at least 3 up-votes. For C: bash and awk code
Teacher 12 days ago, created an answer with at least 3 up-votes. For C: TCGA immunotherapy treated melanoma data
Teacher 12 days ago, created an answer with at least 3 up-votes. For C: TCGA immunotherapy treated melanoma data
Scholar 14 days ago, created an answer that has been accepted. For A: Downsample BAM for targeted NGS panels
Scholar 14 days ago, created an answer that has been accepted. For A: Single-color Agilent array analyzing in R
Teacher 14 days ago, created an answer with at least 3 up-votes. For C: TCGA immunotherapy treated melanoma data
Commentator 15 days ago, created a comment with at least 3 up-votes. For C: how can interpret these biologically weird results?
Commentator 15 days ago, created a comment with at least 3 up-votes. For C: bash and awk code
Appreciated 18 days ago, created a post with more than 5 votes. For R functions for parallel processing
Scholar 18 days ago, created an answer that has been accepted. For A: Single-color Agilent array analyzing in R
Teacher 18 days ago, created an answer with at least 3 up-votes. For C: TCGA immunotherapy treated melanoma data
Teacher 19 days ago, created an answer with at least 3 up-votes. For C: TCGA immunotherapy treated melanoma data
Appreciated 19 days ago, created a post with more than 5 votes. For R functions for parallel processing
Teacher 20 days ago, created an answer with at least 3 up-votes. For C: TCGA immunotherapy treated melanoma data
Scholar 22 days ago, created an answer that has been accepted. For A: Single-color Agilent array analyzing in R
Teacher 23 days ago, created an answer with at least 3 up-votes. For C: TCGA immunotherapy treated melanoma data
Teacher 24 days ago, created an answer with at least 3 up-votes. For C: TCGA immunotherapy treated melanoma data
Teacher 29 days ago, created an answer with at least 3 up-votes. For C: TCGA immunotherapy treated melanoma data

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1133 users visited in the last hour