User: Leonardo Collado Torres
Leonardo Collado Torres • 610
- Reputation:
- 610
- Status:
- Trusted
- Location:
- United States
- Website:
- http://lcolladotor.git...
- Twitter:
- fellgernon
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 month, 2 weeks ago
- Joined:
- 9 years ago
- Email:
- l*******@jhu.edu
Leonardo Collado Torres, Ph. D., Data Scientist
Lieber Institute for Brain Development
Clinical Sciences Division
855 N Wolfe St, Suite 300
Baltimore, MD 21205
Website: http://lcolladotor.github.io/about.html
Blog: http://lcolladotor.github.io/
Posts by Leonardo Collado Torres
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... Thanks for providing a workaround Mike and for debugging this together with Ben!
Best,
Leo
...
written 6 weeks ago by
Leonardo Collado Torres • 610
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... If you have any questions, please let us know!! We are hoping to encourage and enable more R/Bioconductor users to become Bioc contributors/developers.
Best,
Leonardo
...
written 5 months ago by
Leonardo Collado Torres • 610
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... No problem =)
...
written 6 months ago by
Leonardo Collado Torres • 610
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... Hi,
This question is related to https://github.com/leekgroup/recount-website/issues/11.
The following R code
library('recount')
metadata <- all_metadata()
m <- subset(metadata, project == 'SRP000941')
download_study("SRP000941", type = "rse-gene")
load(file.path("SRP000941", "rse_gene.Rdata") ...
written 6 months ago by
Leonardo Collado Torres • 610
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... Hi,
TCGA is not part of SRA, or at least wasn't when recount2 was made. Use the TCGA-specific ids for matching samples there such as gdc_file_id instead of run.
Best,
Leonardo
...
written 6 months ago by
Leonardo Collado Torres • 610
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... Since I don't know any other way of "closing" a question, I'll just say that I failed in this case to provide a reproducible example 3.3 years ago. See https://support.bioconductor.org/p/62026/#105654.
...
written 7 months ago by
Leonardo Collado Torres • 610
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... Sorry, this was so long ago that I don't remember. I even forgot about this thread and as you can see, I never got around to providing a reproducible example. Guess I can use this thread as an example of what not to do in the Bioc support website.
My guess from using `qvalue` in other projects i ...
written 7 months ago by
Leonardo Collado Torres • 610
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... I added this as an example in regionMatrix() to derfinder version 1.13.1. Details: https://github.com/lcolladotor/derfinder/commit/cb7f8bdb9d99aae0a86758aa3e5bde00712a14d6
...
written 9 months ago by
Leonardo Collado Torres • 610
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... Hi,
You can combine the different pieces of regionMat (the one that is a list with one element per chromosome) manually as shown in the code below:
library('derfinder')
## Modified code from ?regionMatrix
## Create some toy data
library('IRanges')
x <- Rle(round(runif(1e4, max=10)))
y <- ...
written 9 months ago by
Leonardo Collado Torres • 610
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258
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... Thanks Aaron!
Best, Leo
...
written 10 months ago by
Leonardo Collado Torres • 610
Latest awards to Leonardo Collado Torres
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Getting a flat metadata table from the XML files in TCGA: is it feasible?
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Trying to use the liftOver function from the rtracklayer package in R 2.14.0
Scholar
15 months ago,
created an answer that has been accepted.
For A: Number of IRanges elements in TCGA HiSeqV2 dataset
Scholar
15 months ago,
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For A: derfinder: fullCoverage() problems
Scholar
15 months ago,
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For A: Issue creating a genomic state object in derfinder from an Ensembl GTF file
Scholar
15 months ago,
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For A: Is it possible to read bigwig files with rtracklayer over https? Comes down to G
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15 months ago,
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For A: derfinder: analyzeChr() breaks on chromosomes > 22
Scholar
15 months ago,
created an answer that has been accepted.
For A: derfinder gets stuck in calculatePvalues
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Getting the metadata for a RNA-seq sample from TCGA when you have the uuid
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15 months ago,
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For Trying to use the liftOver function from the rtracklayer package in R 2.14.0
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15 months ago,
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For A: derfinder gets stuck in calculatePvalues
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For A: derfinder gets stuck in calculatePvalues
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For A: derfinder gets stuck in calculatePvalues
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For A: derfinder: fullCoverage() problems
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3.9 years ago,
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For A: derfinder: fullCoverage() problems
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For A: derfinder: fullCoverage() problems
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For A: derfinder: fullCoverage() problems
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