User: Leonardo Collado Torres
Leonardo Collado Torres • 600
- Reputation:
- 600
- Status:
- Trusted
- Location:
- United States
- Website:
- http://lcolladotor.git...
- Twitter:
- fellgernon
- Scholar ID:
- Google Scholar Page
- Last seen:
- 3 weeks, 1 day ago
- Joined:
- 8 years, 10 months 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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... 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
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written 12 weeks ago by
Leonardo Collado Torres • 600
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... No problem =)
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written 4 months ago by
Leonardo Collado Torres • 600
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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 4 months ago by
Leonardo Collado Torres • 600
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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 4 months ago by
Leonardo Collado Torres • 600
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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 5 months ago by
Leonardo Collado Torres • 600
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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 5 months ago by
Leonardo Collado Torres • 600
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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 7 months ago by
Leonardo Collado Torres • 600
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212
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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 7 months ago by
Leonardo Collado Torres • 600
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... Thanks Aaron!
Best, Leo
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written 7 months ago by
Leonardo Collado Torres • 600
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... Hi,
While I did figure out my main problem, I decided it would still be worth posting just as an example of how completing all the Bioconductor posting guide steps can help users find their own problem.
In my case, when I was writing the last part of my question, I realized that maybe I wasn't co ...
written 7 months ago by
Leonardo Collado Torres • 600
Latest awards to Leonardo Collado Torres
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13 months ago,
created an answer that has been accepted.
For A: Number of IRanges elements in TCGA HiSeqV2 dataset
Popular Question
13 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
Popular Question
13 months ago,
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For Getting the metadata for a RNA-seq sample from TCGA when you have the uuid
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For A: derfinder gets stuck in calculatePvalues
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13 months ago,
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For A: derfinder: analyzeChr() breaks on chromosomes > 22
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13 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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13 months ago,
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For A: Issue creating a genomic state object in derfinder from an Ensembl GTF file
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13 months ago,
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For A: derfinder: fullCoverage() problems
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13 months ago,
created an answer that has been accepted.
For A: derfinder gets stuck in calculatePvalues
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15 months ago,
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16 months ago,
created an answer that has been accepted.
For A: derfinder gets stuck in calculatePvalues
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2.2 years ago,
created 100 posts.
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2.2 years ago,
created an answer that has been accepted.
For A: derfinder gets stuck in calculatePvalues
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3.1 years ago,
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For A: derfinder: fullCoverage() problems
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3.7 years ago,
created an answer that has been accepted.
For A: derfinder: fullCoverage() problems
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3.7 years ago,
created an answer with at least 3 up-votes.
For A: derfinder: fullCoverage() problems
Scholar
3.7 years ago,
created an answer that has been accepted.
For A: derfinder: fullCoverage() problems
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3.8 years ago,
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