User: António Miguel de Jesus Domingues
- Reputation:
- 390
- Status:
- Trusted
- Location:
- Germany
- Website:
- http://adomingues.gith...
- Last seen:
- 2 months, 2 weeks ago
- Joined:
- 6 years, 3 months ago
- Email:
- a***********@gmail.com
Posts by António Miguel de Jesus Domingues
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... I downloaded data for an RNA-seq experiment using the ExpressionAtlas package - very very straightforward by the way. Sadly the data contains only the raw counts from said experiment, whereas my expectation was that one would also get access to the pre-calculated RPKM/TPM since these are available ...
written 7 months ago by
António Miguel de Jesus Domingues • 390
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...
> library(biomaRt)
> packageVersion("biomaRt")
[1] ‘2.35.2’
## [1] 97 3
## [1] "Is drerio present? TRUE"
All systems are go :) Thank you for the fix.
...
written 7 months ago by
António Miguel de Jesus Domingues • 390
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... Good tip. In my case it was a little lazy because I am also using the script to run some C. elegans data analysis and this will work for both - RIPSeeker needs biomaRt/ensembl so I need an archive version before the move to Wormbase. Another hack.
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written 7 months ago by
António Miguel de Jesus Domingues • 390
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... @moderators: I could not format the post properly due to an error:
Language "fr" is not one of the supported languages ['en']!
Post was copy-pasted from a markdown document generated via knitr, so no idea.
...
written 7 months ago by
António Miguel de Jesus Domingues • 390
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... Whilst running a `RIPSeeper` analysis, I noticed that the dataset `drerio_gene_ensembl` which used to be available via `biomaRt` is not longer listed or accessible. To test this I first upgraded my `bioC` to make sure I am working with the latest version of `biomaRt` (2.34.0).
```r
biocLite("BiocU ...
written 7 months ago by
António Miguel de Jesus Domingues • 390
• updated 7 months ago by
Mike Smith • 2.8k
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... It worked, thanks! I wonder if this could be something to add to the vignette? In any case, it is now here for those struggling with the same issue.
...
written 7 months ago by
António Miguel de Jesus Domingues • 390
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... tldr: using derfinder for individual chromosomes works, but merging them using do.call(c) or do.call(rbind) leads to errors. How to perform DRE with all chromosomes?
I have been following the tutorials for derfinder running the analysis for an individual chromosome:
fullCov <- fullCoverage(fil ...
written 7 months ago by
António Miguel de Jesus Domingues • 390
• updated 7 months ago by
Leonardo Collado Torres • 600
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... I am running derfinder to ultimately find DER in a time course but despite the very good documentation I have some doubts about how set the cutoff to find expressed regions. In the 2017 NAR paper, it is stated that an average across all regions and samples is used as a cut-off (Finding ERs):
Here, ...
written 7 months ago by
António Miguel de Jesus Domingues • 390
• updated 7 months ago by
Leonardo Collado Torres • 600
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... > You can see from re-arrangement of terms that your desired ratio is mathematically equal to RFK679 / Tyr101
*faceslap*
Of course. way simpler than I thought. I probably missed those other posts because I was looking specifically at RIP-seq (and ChIP-seq) posts. It turns out I was over-thinkin ...
written 9 months ago by
António Miguel de Jesus Domingues • 390
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... Hi Michael,
Thank you for the quick reply.
Maybe it was not very clear from my post (I rephrased it a little) but there are two parts to my analysis. The first, compare any condition vs N2, is kind of classic and I am following what you suggested, ~condition, followed by:
results(dds, contrast=c("co ...
written 9 months ago by
António Miguel de Jesus Domingues • 390
Latest awards to António Miguel de Jesus Domingues
Popular Question
14 months ago,
created a question with more than 1,000 views.
For ChIPseeker: Error in annotatePeak
Supporter
14 months ago,
voted at least 25 times.
Popular Question
14 months ago,
created a question with more than 1,000 views.
For problems generating a gene2GOlist in topGO
Popular Question
18 months ago,
created a question with more than 1,000 views.
For Gviz - show plus and minus strand from a bam
Appreciated
2.3 years ago,
created a post with more than 5 votes.
For A: Plot ggplot2 and ggbio Images Together
Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For Extend GRanges start/end
Teacher
2.9 years ago,
created an answer with at least 3 up-votes.
For A: Plot ggplot2 and ggbio Images Together
Scholar
3.1 years ago,
created an answer that has been accepted.
For A: Plot ggplot2 and ggbio Images Together
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