User: Leonardo Collado Torres
Leonardo Collado Torres • 690
- Reputation:
- 690
- Status:
- Trusted
- Location:
- United States
- Website:
- http://lcolladotor.git...
- Twitter:
- fellgernon
- Scholar ID:
- Google Scholar Page
- Last seen:
- 2 weeks, 2 days ago
- Joined:
- 10 years, 1 month ago
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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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... Awesome, thanks for sharing the code! =)
Best,
Leo ...
written 16 days ago by
Leonardo Collado Torres • 690
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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 20 days ago by
Leonardo Collado Torres • 690
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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 26 days ago by
Leonardo Collado Torres • 690
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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 5 weeks ago by
Leonardo Collado Torres • 690
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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 5 weeks ago by
Leonardo Collado Torres • 690
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... Hi,
I just wanted to check in and see if you've resolved this question. If not, please post a reproducible example so I and others can help you.
Best,
Leonardo ...
written 5 weeks ago by
Leonardo Collado Torres • 690
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... Hi,
I never got an email for this thread since the `recount` tag was not used initially.
In any case, I updated `recount::geo_characteristics()` in version 1.10.12 (BioC 3.9 -- current release) and 1.11.12 (BioC 3.10 -- current devel) such that now, with your code the following runs.
```R
stopifn ...
written 5 weeks ago by
Leonardo Collado Torres • 690
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... Ansker by @jmfu:
```
Hi there,
* "ses" is the standard errors of the fragments estimates,
* "scores" is score between 0 and 1 that dictates how uniquely identifiable each transcript is under the model we fit (0 being perfectly redundant, and 1 being perfectly unique)
* "df" is the degrees of freed ...
written 5 weeks ago by
Leonardo Collado Torres • 690
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... ```R
download_study('SRP009615', type = 'samples')
2019-08-15 15:25:04 downloading file SRR387777.bw to SRP009615/bw
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387777.bw'
Content type 'text/plain; charset=UTF-8' length 94700336 bytes (90.3 MB)
downloaded 90.3 MB
2019-08-15 15:25:15 ...
written 8 weeks ago by
Leonardo Collado Torres • 690
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... ```R
hms 0.5.0 2019-07-09 [1] CRAN (R 3.6.1)
htmlTable 1.13.1 2019-01-07 [1] CRAN (R 3.6.1)
htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.6.1)
htmlwidgets 1.3 2018-09-30 [1] CRAN (R 3.6.1)
httr 1.4.1 2019- ...
written 8 weeks ago by
Leonardo Collado Torres • 690
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For Trying to use the liftOver function from the rtracklayer package in R 2.14.0
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