Moderator: Kevin Blighe
Kevin Blighe ♦ 41k
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- Guy's Hospital, London
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- 1 year, 7 months ago
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Do not worry... I am Irish.
'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:
Posts by Kevin Blighe
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Comment:
C: Convert gff.gz file to gtf
... gunzip GCF_000697945.2_Focc_2.1_genomic.gff.gz ...
written 1 hour ago by
Kevin Blighe ♦ 41k
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... > 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 Blighe ♦ 41k
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... 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 Blighe ♦ 41k
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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 Blighe ♦ 41k
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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 Blighe ♦ 41k
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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 Blighe ♦ 41k
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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 Blighe ♦ 41k
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...
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 Blighe ♦ 41k
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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 Blighe ♦ 41k
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... 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 Blighe ♦ 41k
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