User: Leonardo Collado Torres

gravatar for Leonardo Collado Torres
Reputation:
610
Status:
Trusted
Location:
United States
Website:
http://lcolladotor.git...
Twitter:
fellgernon
Scholar ID:
Google Scholar Page
Last seen:
1 week, 1 day ago
Joined:
9 years, 7 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 • 180 results • page 1 of 18 • next >
0
votes
2
answers
83
views
2
answers
Comment: C: Recount data for unannotated genes
... Thanks for posting this answer Chris! Best, Leo ...
written 8 days ago by Leonardo Collado Torres • 610
0
votes
1
answer
57
views
1
answers
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 Torres • 610
0
votes
2
answers
83
views
2
answers
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 Torres • 610
0
votes
1
answer
229
views
1
answers
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 Torres • 610
1
vote
1
answer
229
views
1
answer
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 Torres • 610 • updated 4 months ago by Martin Morgan ♦♦ 23k
0
votes
0
answers
132
views
0
answers
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 Torres • 610
0
votes
1
answer
229
views
1
answers
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 Torres • 610
0
votes
1
answer
183
views
1
answers
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 Torres • 610
0
votes
1
answer
181
views
1
answers
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 Torres • 610
1
vote
0
answers
579
views
0
answers
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 Torres • 610

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 5 months 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 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
Supporter 2.0 years ago, voted at least 25 times.
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 gets stuck in calculatePvalues
Centurion 3.0 years ago, created 100 posts.
Scholar 3.9 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 4.5 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 4.5 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: derfinder: fullCoverage() problems
Autobiographer 4.6 years ago, has more than 80 characters in the information field of the user's profile.
Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 204 users visited in the last hour