User: Leonardo Collado Torres

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590
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Location:
United States
Website:
http://lcolladotor.git...
Twitter:
fellgernon
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Last seen:
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8 years, 5 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 • 167 results • page 2 of 17 • next >
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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 4 months ago by Leonardo Collado Torres590
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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 5 months ago by Leonardo Collado Torres590
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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 5 months ago by Leonardo Collado Torres590
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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 5 months ago by Leonardo Collado Torres590
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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 5 months ago by Leonardo Collado Torres590
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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 5 months ago by Leonardo Collado Torres590
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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$gd ...
written 5 months ago by Leonardo Collado Torres590
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Comment: C: IRanges error from derfinder analyzeChr with custom TxDb?
... I normally set both to the same value when loading and when running analyzeChr(). analyzeChr() will only filter again if `colsubset` is used, which sometimes I need to use and others I don't. So setting the cutoff when loading and when running analyzeChr() saves me the trouble of remembering to use/ ...
written 6 months ago by Leonardo Collado Torres590
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Answer: A: IRanges error from derfinder analyzeChr with custom TxDb?
... Hi, The following code reproduces the problem. library('derfinder') datadir <- system.file('extdata', 'genomeData', package='derfinder') files <- rawFiles(datadir = datadir, samplepatt = '*accepted_hits.bam$', fileterm = NULL) ## Shorten the column names names(files) <- gsub('_acce ...
written 6 months ago by Leonardo Collado Torres590

Latest awards to Leonardo Collado Torres

Scholar 8 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Supporter 10 months ago, voted at least 25 times.
Scholar 11 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Scholar 22 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Centurion 22 months ago, created 100 posts.
Scholar 2.7 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 3.3 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: derfinder: fullCoverage() problems
Scholar 3.3 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Autobiographer 3.4 years ago, has more than 80 characters in the information field of the user's profile.

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