User: Leonardo Collado Torres

Reputation:
600
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Trusted
Location:
United States
Website:
http://lcolladotor.git...
Twitter:
fellgernon
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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

<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 12 weeks ago by Leonardo Collado Torres600
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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 4 months ago by Leonardo Collado Torres600
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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 4 months ago by Leonardo Collado Torres600
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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 5 months ago by Leonardo Collado Torres600
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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 5 months ago by Leonardo Collado Torres600
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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 7 months ago by Leonardo Collado Torres600
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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 7 months ago by Leonardo Collado Torres600
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Comment: C: Time-course group difference analysis with repeated individuals using limma-voom
... Thanks Aaron! Best, Leo ...
written 7 months ago by Leonardo Collado Torres600
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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 7 months ago by Leonardo Collado Torres600

Latest awards to Leonardo Collado Torres

Scholar 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, 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
Scholar 13 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Scholar 13 months ago, created an answer that has been accepted. For A: derfinder: analyzeChr() breaks on chromosomes > 22
Scholar 13 months ago, created an answer that has been accepted. For A: Is it possible to read bigwig files with rtracklayer over https? Comes down to G
Scholar 13 months ago, created an answer that has been accepted. For A: Issue creating a genomic state object in derfinder from an Ensembl GTF file
Scholar 13 months ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 13 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Supporter 15 months ago, voted at least 25 times.
Scholar 16 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Centurion 2.2 years ago, created 100 posts.
Scholar 2.2 years ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Scholar 3.1 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 3.7 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Teacher 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
Autobiographer 3.8 years ago, has more than 80 characters in the information field of the user's profile.

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