User: Leonardo Collado Torres

Reputation:
590
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Trusted
Location:
United States
Website:
http://lcolladotor.git...
Twitter:
fellgernon
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Last seen:
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Joined:
8 years, 7 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

<prev • 171 results • page 1 of 18 • next >
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Comment: C: Latin American BioC Developers Workshop 2018
... 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 3 days ago by Leonardo Collado Torres590
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Answer: A: According to Recount2 metadata and Recount2 website, SRP000941 has 345 samples,
... 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 5 weeks ago by Leonardo Collado Torres590
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Answer: A: Recount2 TCGA metadata missing sample, run and experiment columns
... 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 7 weeks ago by Leonardo Collado Torres590
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Answer: A: Hm... segfault when using qvalue 1.39.1, has anyone else encountered this?
... 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 10 weeks ago by Leonardo Collado Torres590
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Comment: C: Hm... segfault when using qvalue 1.39.1, has anyone else encountered this?
... 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 10 weeks ago by Leonardo Collado Torres590
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Comment: C: derfinder: how to merge regions and counts from individual chromosomes
... I added this as an example in regionMatrix() to derfinder version 1.13.1. Details: https://github.com/lcolladotor/derfinder/commit/cb7f8bdb9d99aae0a86758aa3e5bde00712a14d6 ...
written 4 months ago by Leonardo Collado Torres590
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Answer: A: derfinder: how to merge regions and counts from individual chromosomes
... 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 4 months ago by Leonardo Collado Torres590
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Comment: C: Time-course group difference analysis with repeated individuals using limma-voom
... Thanks Aaron! Best, Leo ...
written 4 months ago by Leonardo Collado Torres590
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Comment: C: Time-course group difference analysis with repeated individuals using limma-voom
... 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 5 months ago by Leonardo Collado Torres590

Latest awards to Leonardo Collado Torres

Scholar 10 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Supporter 12 months ago, voted at least 25 times.
Scholar 13 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Scholar 24 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Centurion 24 months ago, created 100 posts.
Scholar 2.8 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 3.4 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: derfinder: fullCoverage() problems
Scholar 3.5 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Autobiographer 3.6 years ago, has more than 80 characters in the information field of the user's profile.

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