User: Leonardo Collado Torres

Reputation:
600
Status:
Trusted
Location:
United States
Website:
http://lcolladotor.git...
Twitter:
fellgernon
Scholar ID:
Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
8 years, 9 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 • 171 results • page 2 of 18 • next >
1
vote
1
answer
223
views
1
answer
Time-course group difference analysis with repeated individuals using limma-voom
... Hi, From the limmaUsersGuide() section "9.7 Multi-level Experiments" I learned about using duplicateCorrelation() and passing that information to lmFit() to handle observations from the same individual (using block and correlation arguments). Similarly, from "9.6.2 Many time points" I learned about ...
limma written 7 months ago by Leonardo Collado Torres600 • updated 7 months ago by Aaron Lun20k
0
votes
1
answers
176
views
1
answers
Answer: A: derfinder mean Expressed Region cutoff
... Hi, Maybe the wording in the paper could have been clearer. Once you have a mean coverage vector (in reality a Rle object), we use a single global cutoff for finding the expressed regions. Just like in Figure 2A of the derfinder paper https://academic.oup.com/nar/article/45/2/e9/2953306.  For choo ...
written 7 months ago by Leonardo Collado Torres600
0
votes
1
answers
220
views
1
answers
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 months ago by Leonardo Collado Torres600
0
votes
0
answers
268
views
0
answers
Comment: C: NA values of count matrix in class DESeqDataSet
... Looks like the same as this question https://support.bioconductor.org/p/100791 ...
written 8 months ago by Leonardo Collado Torres600
0
votes
0
answers
229
views
0
answers
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 8 months ago by Leonardo Collado Torres600
0
votes
0
answers
207
views
0
answers
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 ...
0
votes
1
answers
344
views
1
answers
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 9 months ago by Leonardo Collado Torres600
0
votes
1
answers
271
views
1
answers
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 9 months ago by Leonardo Collado Torres600
0
votes
1
answers
271
views
1
answers
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 9 months ago by Leonardo Collado Torres600
0
votes
1
answers
225
views
1
answers
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 9 months ago by Leonardo Collado Torres600

Latest awards to Leonardo Collado Torres

Scholar 12 months ago, created an answer that has been accepted. For A: Number of IRanges elements in TCGA HiSeqV2 dataset
Popular Question 12 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 12 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
Scholar 12 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Scholar 12 months ago, created an answer that has been accepted. For A: derfinder: analyzeChr() breaks on chromosomes > 22
Scholar 12 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 12 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 12 months ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 12 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Supporter 14 months ago, voted at least 25 times.
Scholar 16 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Centurion 2.2 years ago, created 100 posts.
Scholar 2.2 years ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Scholar 3.0 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 3.6 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: derfinder: fullCoverage() problems
Scholar 3.7 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Autobiographer 3.8 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 271 users visited in the last hour