User: Leonardo Collado Torres

gravatar for 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 • 177 results • page 1 of 18 • next >
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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 14 days ago by Leonardo Collado Torres • 610
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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 14 days ago by Leonardo Collado Torres • 610 • updated 14 days ago by Martin Morgan ♦♦ 22k
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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 4 weeks ago by Leonardo Collado Torres • 610
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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 7 weeks ago by Leonardo Collado Torres • 610
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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 11 weeks ago by Leonardo Collado Torres • 610
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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 4 months ago by Leonardo Collado Torres • 610
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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 7 months ago by Leonardo Collado Torres • 610
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Comment: C: According to Recount2 metadata and Recount2 website, SRP000941 has 345 samples,
... No problem =) ...
written 9 months ago by Leonardo Collado Torres • 610
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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 9 months ago by Leonardo Collado Torres • 610
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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 9 months ago by Leonardo Collado Torres • 610

Latest awards to Leonardo Collado Torres

Popular Question 6 weeks 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 6 weeks ago, created a question with more than 1,000 views. For Is it possible to read bigwig files with rtracklayer over https? Comes down to GenomeInfoDb::seqinfo()
Popular Question 7 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 7 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 17 months ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 17 months ago, created an answer that has been accepted. For A: Number of IRanges elements in TCGA HiSeqV2 dataset
Scholar 17 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 17 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 17 months ago, created an answer that has been accepted. For A: derfinder: analyzeChr() breaks on chromosomes > 22
Scholar 17 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Popular Question 17 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 17 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 18 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
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Scholar 3.5 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
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