User: Kevin Blighe

gravatar for Kevin Blighe
Kevin Blighe190
Reputation:
190
Status:
Trusted
Location:
Website:
https://github.com/kev...
Twitter:
@biostar41557
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Google Scholar Page
Last seen:
2 hours ago
Joined:
1 year, 2 months ago
Email:
k****@clinicalbioinformatics.co.uk

*also Moderator on Biostars: biostar41557

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.

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'Incrocio le dita e spero'

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

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Developer / Maintainer of Bioconductor packages:

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

 

Posts by Kevin Blighe

<prev • 69 results • page 1 of 7 • next >
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Comment: C: Combining different arrays in analysis
... Cross-posted: https://www.biostars.org/p/398240/ ...
written 4 days ago by Kevin Blighe190
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Comment: C: Rsamtools::scanBam ends prematurely under Windows 10
... Hey Gordon, I'm using Windows 10 and Ubuntu 16.04. Loading a fresh session and doing nothing other than load *Rsamtools*, I tested a 'small' (~50MB) and 'large' (~5GB) BAM, and got the following: Windows 10 ------ s <- scanBam("test1.bam",param=ScanBamParam(what="rname")) length(s[[1]]$ ...
written 4 days ago by Kevin Blighe190
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Comment: C: WGCNA gene clusters vs eigengenes
... This was cross-posted (and answered) on Biostars: https://www.biostars.org/p/397668/ Also note that WGCNA is not a Bioconductor package; however, one of the WGCNA developers is a member here, and may answer WGCNA-related questions. ...
written 6 days ago by Kevin Blighe190
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Comment: C: DESeq2 lfcShrink warning use ashr method
... Mike, we directed the user here, as we were unsure about this one. I personally had not seen that warning message before. https://www.biostars.org/p/397274/ ...
written 8 days ago by Kevin Blighe190
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Answer: A: Coding vs Noncoding Genes in Hit List
... Hey, *biomaRt* is one solution. Take a look at this example, starting with HGNC symbols: genes <- c('BRCA1', 'XIST', 'TXNIP', 'AFG3L1P') require(biomaRt) mart <- useMart("ENSEMBL_MART_ENSEMBL", host = "useast.ensembl.org") mart <- useDataset("hsapiens_gene_ensembl", m ...
written 8 days ago by Kevin Blighe190
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Comment: C: ggbio - change transcript label sizes
... Great - thanks for the information, Michael. ...
written 21 days ago by Kevin Blighe190
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ggbio - change transcript label sizes
... It seems next to impossible to change the size of the `geom_text()` labels with `autoplot()` in *ggbio*. For example, take the reproducible code: require(ggbio) require(GenomicRanges) require(Mus.musculus) p <- autoplot( Mus.musculus, # OrganismDb class which = ...
annotation ggbio written 22 days ago by Kevin Blighe190 • updated 21 days ago by Michael Lawrence11k
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Comment: C: Determining survival correlation among probes
... Cross-posted: https://www.biostars.org/p/392859/ ...
written 6 weeks ago by Kevin Blighe190
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Comment: C: RNA-Seq normalization for co-expression analysis
... Typically, we filter the raw counts, then normalise, and then make statistical inferences on the normalised counts. After that, we may apply a further transformation on the normalised counts for the purposes of conducting downstream analyses. ...
written 8 weeks ago by Kevin Blighe190
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Comment: C: RNA-Seq normalization for co-expression analysis
... I see. Gordon has already answered. Based on your logic, you have CPM counts, and then you apply TMM to those? ...
written 9 weeks ago by Kevin Blighe190

Latest awards to Kevin Blighe

Supporter 8 months ago, voted at least 25 times.
Autobiographer 14 months ago, has more than 80 characters in the information field of the user's profile.

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