User: Leonardo Collado Torres

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

<prev • 172 results • page 1 of 18 • next >
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Comment: C: DESeq2 error: "vector: cannot make a vector of mode 'S4'"
... Thanks for providing a workaround Mike and for debugging this together with Ben! Best, Leo ...
written 6 weeks ago by Leonardo Collado Torres610
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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 5 months ago by Leonardo Collado Torres610
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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 6 months ago by Leonardo Collado Torres610
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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 6 months ago by Leonardo Collado Torres610
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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 7 months ago by Leonardo Collado Torres610
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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 7 months ago by Leonardo Collado Torres610
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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 9 months ago by Leonardo Collado Torres610
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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 9 months ago by Leonardo Collado Torres610
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Comment: C: Time-course group difference analysis with repeated individuals using limma-voom
... Thanks Aaron! Best, Leo ...
written 10 months ago by Leonardo Collado Torres610

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, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 15 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 15 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 15 months ago, created an answer that has been accepted. 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
Popular Question 15 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: derfinder gets stuck in calculatePvalues
Supporter 17 months ago, voted at least 25 times.
Scholar 19 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Scholar 2.4 years ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
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Scholar 3.3 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
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Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: derfinder: fullCoverage() problems
Scholar 3.9 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
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