User: Kevin Blighe

gravatar for Kevin Blighe
Kevin Blighe40
Reputation:
40
Status:
New User
Location:
Republic of Ireland
Website:
https://github.com/kev...
Twitter:
KevinBlighe
Scholar ID:
Google Scholar Page
Last seen:
1 day, 2 hours ago
Joined:
8 months, 1 week ago
Email:
k****@clinicalbioinformatics.co.uk

*also Moderator on Biostars: biostar41557

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

Developer / Maintainer of Bioconductor packages:

Posts by Kevin Blighe

<prev • 28 results • page 1 of 3 • next >
0
votes
1
answer
65
views
1
answers
Comment: C: bplapply - only SerialParam or single worker Multicore working on R/macos 10.14
... I have posted various answers on Biostars about how to correctly use parallel processing enabled functions in R; however, I do not cover bplapply. On Windows, the equivalent to `lapply` is `parLapply`; on Mac/Linux, it is `mclapply` - R functions for parallel processing - Snowfall Parallelisation ...
written 5 days ago by Kevin Blighe40
0
votes
1
answer
76
views
1
answers
Comment: C: Dunn Index for Clusters from scRNA-Seq
... Cross-posted on Biostars: https://www.biostars.org/p/368557/ ...
written 9 days ago by Kevin Blighe40
1
vote
0
answers
68
views
0
answers
Comment: C: co-expresson network between LncRNA-mRNA
... Also posted on Biostars, twice: https://www.biostars.org/p/368571/ & https://www.biostars.org/p/368582/ ...
written 9 days ago by Kevin Blighe40
0
votes
1
answer
86
views
1
answers
Answer: A: Heatmap of RPKM analysis
... You are using the basic `heatmap()` function. If my memory serves me correctly, by default, row and column names are not activated in this function. You can specify them with `labRow` and `labCol`. You are also using `as.matrix()`, but I believe you should use `data.matrix()`. If you want to 'upgr ...
written 24 days ago by Kevin Blighe40
0
votes
0
answers
59
views
0
answers
Comment: C: Bioconductor and WGS: recommended practices?
... Hey Vince, not that I am of. Outside of VCF and R, there is the tab-delimited Mutation Annotation Format (MAF), but I'm not sure it has really caught on. Generally, I think that Bioconductor could benefit from having much more variant / mutation datasets, like: - 1000 Genomes, ExAc, etc - COSMIC ...
written 5 weeks ago by Kevin Blighe40
0
votes
1
answer
120
views
1
answers
Comment: C: How to generate a volcano plot when p-values from DESeq2 are zero?
... That functionality is not available, unfortunately. Regarding the fundamental issue: I don't know what a p-value of 0 actually means. You could likely identify these transcripts prior to running EnhancedVolcano and set them to, for example, 10E-1 * the lowest non-zero p-value. Then, the plot visuali ...
written 5 weeks ago by Kevin Blighe40
0
votes
1
answer
120
views
1
answers
Comment: C: How to generate a volcano plot when p-values from DESeq2 are zero?
... The package is built on the ggplot2 engine and returns a ggplot2 object, so, you could likely just do, for example: ``` EnhancedVolcano(...) + coord_cartesian(-log10(10E-50), -log10(10E-60)) ``` Behaviour may be unexpected though. ...
written 5 weeks ago by Kevin Blighe40
0
votes
1
answer
120
views
1
answers
Comment: C: How to generate a volcano plot when p-values from DESeq2 are zero?
... I'll just add a comment on the volcano part because you have tagged my package, *EnhancedVolcano*. *EnhancedVolcano* will automatically convert p-values of 0 to the lowest possible machine value, which I imagine differs based on whatever OS you are using. It issues a warning message to console when ...
written 5 weeks ago by Kevin Blighe40
0
votes
0
answers
104
views
0
answers
Comment: C: Oligo RMA normalization : ERROR; return code from pthread_create() is 22
... If you're running it on a cluster environment (running Red Hat), then you may be up against restrictions in place by your system administrator. Are you just running it from the command line on the server? ...
written 7 weeks ago by Kevin Blighe40
0
votes
1
answer
87
views
1
answers
Answer: A: GWAS power and sample size calculation
... Here are my answers, on Biostars: - https://www.biostars.org/p/281585/#281596 - https://www.biostars.org/p/356879/#356988 Only 1 of these is R, and it is not a Bioconductor package. Kevin ...
written 7 weeks ago by Kevin Blighe40

Latest awards to Kevin Blighe

Autobiographer 8 months ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 353 users visited in the last hour