User: Leonardo Collado Torres
Leonardo Collado Torres • 710
- Reputation:
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- Location:
- United States
- Website:
- http://lcolladotor.git...
- Twitter:
- fellgernon
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- Joined:
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Leonardo Collado Torres, Ph. D., Staff Scientist
Lieber Institute for Brain Development
855 N Wolfe St, Suite 300
Baltimore, MD 21205
Website: http://lcolladotor.github.io/
Posts by Leonardo Collado Torres
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... This is a separate question, please post a new question Daniel. Thank you =) ...
written 8 days ago by
Leonardo Collado Torres • 710
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... Then you need to look at resources outside of `recount`, say, ENSEMBL, to check which is the particular gene ID you want based on the gene structure. It's not rare for two Ensembl IDs to match to the same gene symbol. ...
written 5 weeks ago by
Leonardo Collado Torres • 710
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... Thanks for this answer James! ...
written 5 weeks ago by
Leonardo Collado Torres • 710
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... ## R 3.4.4
```R
> genes <- c('ENSG00000283638', 'ENSG00000015479', 'ENSG00000280987')
> AnnotationDbi::mapIds(org.Hs.eg.db::org.Hs.eg.db,
+ genes, 'SYMBOL', 'ENSEMBL',
+ multiVals = 'CharacterList')
'select()' returned 1:1 mapping between keys and columns
CharacterList of length 3 ...
written 5 weeks ago by
Leonardo Collado Torres • 710
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... Hi Sheldon,
The gene symbols in `recount` were obtained using this code https://github.com/leekgroup/recount/blob/master/R/reproduce_ranges.R#L95-L97 that relies on `AnnotationDbi::mapIds()` and `org.Hs.eg.db::org.Hs.eg.db`, which I adapted below for the case you report.
```R
genes <- c('ENSG00 ...
written 5 weeks ago by
Leonardo Collado Torres • 710
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... Awesome, thanks for sharing the code! =)
Best,
Leo ...
written 11 weeks ago by
Leonardo Collado Torres • 710
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... The length of `files` mattered regarding the `filter` option. Looks like it's all resolved now though =) Though I'll say it again: you don't need to use `totalMapped` and `targetSize` more than once (so either in `fullCoverage()` or in `regionMatrix()` but not both). ...
written 11 weeks ago by
Leonardo Collado Torres • 710
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... Hi,
It seems that you are normalizing your data twice, no? The file name for the third track includes `normalized`. If that's the case, you don't need to use `derfinder` to scale the data again to a given library size. That is, don't specify `totalMapped` (leave it with the default value of `NULL`) ...
written 12 weeks ago by
Leonardo Collado Torres • 710
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... Hi,
Can you rephrase your question please? I’ didn’t understand what you were asking.
Like, what do you mean by learning that GTEx BigWig files are distributed with multiple SRPs? Is that from recount or some code you ran or from another website/tool? Are you talking about GTEx v6 RNA-seq sample ...
written 3 months ago by
Leonardo Collado Torres • 710
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... Hi @codden.c,
## Question 1
Regarding the first question, I know that there's this https://github.com/sonali-bioc/UncertaintyRNA/blob/master/03_Creating_TPM_TCGA_Data_objects.Rmd#L206 which was used in https://www.biorxiv.org/content/10.1101/445601v2 by Sonali Arora et al. That is, they used the f ...
written 3 months ago by
Leonardo Collado Torres • 710
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For Trying to use the liftOver function from the rtracklayer package in R 2.14.0
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