User: Leonardo Collado Torres

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http://lcolladotor.git...
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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 • 180 results • page 1 of 18 • next >
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Comment: C: Recount data for unannotated genes
... Thanks for posting this answer Chris! Best, Leo ...
written 8 days ago by Leonardo Collado Torres610
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Answer: A: Number of reads from recount are greater than target library size (40 million)
... Hi Sheldon, Apologies for the delay in answering. I was busy trying to finish a paper myself. The answer is a bit complicated. The short version is that some base pairs of the genome are counted more than once in recount2's gene level files. Within a given gene, a base pair is counted only once as ...
written 14 days ago by Leonardo Collado Torres610
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Answer: A: Recount data for unannotated genes
... Hi Francesco, Apologies for the delay in answering. I was busy trying to finish a paper myself. The recount2 project includes base pair coverage BigWig files (see https://f1000research.com/articles/6-1558/v1 for more details on this) that you can leverage to explore any new annotation or un-annota ...
written 15 days ago by Leonardo Collado Torres610
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Comment: C: Error with untar2 that blocks the installation of GO.db on Windows (R 3.5, Bioc
... RS has a 2nd Windows computer and with a fresh install of R 3.5.1 and Bioconductor 3.8 he got a different error: R version 3.5.1 (2018-07-02) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ...
written 4 months ago by Leonardo Collado Torres610
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Error with untar2 that blocks the installation of GO.db on Windows (R 3.5, Bioc 3.8) for using clusterProfiler
... Hi, A colleague of mine (RS) is trying to install the clusterProfiler package that depends on GO.db on his Windows laptop using R 3.5 and Bioconductor 3.8. We haven't been able to install it via BiocManager::install() due to an error with untar2(). If we download the source .tar.gz file on my macOS ...
clusterprofiler go.db written 4 months ago by Leonardo Collado Torres610 • updated 4 months ago by Martin Morgan ♦♦ 23k
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Comment: C: What assays are distributed with Recount TX data
... Yup, please do so Jack! ^^ This info gets reflected at the top of the package page http://bioconductor.org/packages/release/bioc/html/recount.html   Thanks! ...
written 5 months ago by Leonardo Collado Torres610
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Answer: A: Is GTEx age and sex data available via the recount package?
... Hi @abe, Under the metadata section in https://f1000research.com/articles/6-1558/v1 we state that " we compiled metadata for GTEx using the v6 phenotype information available at gtexportal.org". This was also mentioned in the supplementary material of the recount2 paper https://www.nature.com/artic ...
written 6 months ago by Leonardo Collado Torres610
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Answer: A: What does scaling RNASeq data using the area under coverage information (AUC) me
... Hi, I don't know why I didn't get an email about this question. In any case, please check the recount workflow (http://bioconductor.org/packages/release/workflows/html/recountWorkflow.html) published at F1000 Research https://f1000research.com/articles/6-1558/v1. That workflow describes in more det ...
written 6 months ago by Leonardo Collado Torres610
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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 8 months 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 12 months ago by Leonardo Collado Torres610

Latest awards to Leonardo Collado Torres

Popular Question 5 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 11 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 11 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 22 months ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 22 months ago, created an answer that has been accepted. For A: Number of IRanges elements in TCGA HiSeqV2 dataset
Scholar 22 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 22 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 22 months ago, created an answer that has been accepted. For A: derfinder: analyzeChr() breaks on chromosomes > 22
Scholar 22 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Popular Question 22 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 22 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 22 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
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Scholar 3.9 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
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