User: Leonardo Collado Torres

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540
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Location:
United States
Website:
http://lcolladotor.git...
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fellgernon
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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 • 159 results • page 1 of 16 • next >
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Answer: A: Getting pheno tables from recount datasets without any NA values in characterist
... Hi Mustafa, Nearly 13k samples from the SRA ones don't have any characteristics or GEO accession numbers as shown with the code below. There's nothing we can really do about it. Sometimes updates in SRAdb include new GEO accession numbers. The issue with sample metadata being incomplete is a proble ...
written 7 days ago by Leonardo Collado Torres540
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Comment: C: NA values of count matrix in class DESeqDataSet
... Looks like the same as this question https://support.bioconductor.org/p/100791 ...
written 7 weeks ago by Leonardo Collado Torres540
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Comment: C: NA values of count matrix in class DESeqDataSet
... Hi, Please post code for reproducing the error and the R session information you have. Thanks. Also, why are you writing the colData() information to a text file and then reading it back into R? Are you editing the colData() information outside R? Best, Leonardo ...
written 7 weeks ago by Leonardo Collado Torres540
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Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem
... Hi, The following code used to work in R 3.3 with Bioconductor 3.4. It now fails on a linux machine I have access to with both Bioc 3.5 and 3.6 but works in my OSX laptop with the same versions. library(bumphunter) library(TxDb.Hsapiens.UCSC.hg38.knownGene) gene <- annotateTranscripts(txdb = T ...
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Answer: A: Recount TCGA data
... Hi, The text files are missing the gene ids. I realize this is an inconvenience if you don't want to use R. This information is much more well organized in the RangedSummarizedExperiment objects (RSE) that you can download from https://jhubiostatistics.shinyapps.io/recount/ or via the recount Bioc ...
written 10 weeks ago by Leonardo Collado Torres540
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Comment: C: How to preserve the strand of coverage in derfinder::regionMatrix() ?
... https://bioconductor.org/packages/release/bioc/vignettes/derfinder/inst/doc/derfinder-users-guide.html#controlling-loading-from-bam-files ...
written 10 weeks ago by Leonardo Collado Torres540
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Answer: A: How to preserve the strand of coverage in derfinder::regionMatrix() ?
... Hi, If you have stranded RNA-seq data you have to process each strand separately. If you have BAM files, that means using the appropriate Rsamtools::scanBamFlag() information. If you have BigWig files for each strand, then that means importing the data for one strand at a time. You can then add the ...
written 10 weeks ago by Leonardo Collado Torres540
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Comment: C: Matching columns to sample names
... Hi Ben, I think that it'll be best that you contact the TCGA team regarding searching the gdc_file_id's via their web interface (gdc data portal). I don't know if it's a uppercase vs lowercase issue or how their search portal works.  Regarding the TCGA prostate data in recount2, right now you can ...
written 10 weeks ago by Leonardo Collado Torres540
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Comment: C: Matching columns to sample names
... Hi Dorothy, Please check the posting guidelines and create a new post with a reproducible example & session information. Also, use the DESeq2 tag because this has nothing to do with recount from what I can see. Best, Leonardo ...
written 10 weeks ago by Leonardo Collado Torres540
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Answer: A: Matching columns to sample names
... Hi, There are many id columns in the TCGA recount2 metadata. You can access the metadata using colData(rse) or get the metadata for all TCGA samples with all_metadata() as shown below. We used gdc_file_id to match across different tables. library('recount') m <- all_metadata('tcga') head(m$gd ...
written 12 weeks ago by Leonardo Collado Torres540

Latest awards to Leonardo Collado Torres

Scholar 5 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Supporter 7 months ago, voted at least 25 times.
Scholar 8 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Scholar 19 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Centurion 19 months ago, created 100 posts.
Scholar 2.4 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 3.0 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: derfinder: fullCoverage() problems
Scholar 3.1 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
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