User: Leonardo Collado Torres

Reputation:
690
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Trusted
Location:
United States
Website:
http://lcolladotor.git...
Twitter:
fellgernon
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Google Scholar Page
Last seen:
2 weeks, 2 days ago
Joined:
10 years, 1 month ago
Email:
l**********@gmail.com

Leonardo Collado Torres, Ph. D., Staff Scientist
Lieber Institute for Brain Development
855 N Wolfe St, Suite 300
Baltimore, MD 21205

Website: http://lcolladotor.github.io/

 

Posts by Leonardo Collado Torres

<prev • 194 results • page 1 of 20 • next >
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Comment: C: Detection of large regions of expression
... Awesome, thanks for sharing the code! =) Best, Leo ...
written 16 days ago by Leonardo Collado Torres690
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Comment: C: Detection of large regions of expression
... The length of `files` mattered regarding the `filter` option. Looks like it's all resolved now though =) Though I'll say it again: you don't need to use `totalMapped` and `targetSize` more than once (so either in `fullCoverage()` or in `regionMatrix()` but not both). ...
written 20 days ago by Leonardo Collado Torres690
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Answer: A: Detection of large regions of expression
... Hi, It seems that you are normalizing your data twice, no? The file name for the third track includes `normalized`. If that's the case, you don't need to use `derfinder` to scale the data again to a given library size. That is, don't specify `totalMapped` (leave it with the default value of `NULL`) ...
written 26 days ago by Leonardo Collado Torres690
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Comment: C: How to identify all SRPs with GTEx bigwig files?
... Hi, Can you rephrase your question please? I’ didn’t understand what you were asking. Like, what do you mean by learning that GTEx BigWig files are distributed with multiple SRPs? Is that from recount or some code you ran or from another website/tool? Are you talking about GTEx v6 RNA-seq sample ...
written 5 weeks ago by Leonardo Collado Torres690
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Answer: A: Obtaining recount project data in TPM?
... Hi @codden.c, ## Question 1 Regarding the first question, I know that there's this https://github.com/sonali-bioc/UncertaintyRNA/blob/master/03_Creating_TPM_TCGA_Data_objects.Rmd#L206 which was used in https://www.biorxiv.org/content/10.1101/445601v2 by Sonali Arora et al. That is, they used the f ...
written 5 weeks ago by Leonardo Collado Torres690
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Comment: C: NA values of count matrix in class DESeqDataSet
... Hi, I just wanted to check in and see if you've resolved this question. If not, please post a reproducible example so I and others can help you. Best, Leonardo ...
written 5 weeks ago by Leonardo Collado Torres690
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Answer: A: Inconsistent geo_char for rse_tx
... Hi, I never got an email for this thread since the `recount` tag was not used initially. In any case, I updated `recount::geo_characteristics()` in version 1.10.12 (BioC 3.9 -- current release) and 1.11.12 (BioC 3.10 -- current devel) such that now, with your code the following runs. ```R stopifn ...
written 5 weeks ago by Leonardo Collado Torres690
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Answer: A: What assays are distributed with Recount TX data
... Ansker by @jmfu: ``` Hi there, * "ses" is the standard errors of the fragments estimates, * "scores" is score between 0 and 1 that dictates how uniquely identifiable each transcript is under the model we fit (0 being perfectly redundant, and 1 being perfectly unique) * "df" is the degrees of freed ...
written 5 weeks ago by Leonardo Collado Torres690
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Comment: C: how to download bigwig from recount2?
... ```R download_study('SRP009615', type = 'samples') 2019-08-15 15:25:04 downloading file SRR387777.bw to SRP009615/bw trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387777.bw' Content type 'text/plain; charset=UTF-8' length 94700336 bytes (90.3 MB) downloaded 90.3 MB 2019-08-15 15:25:15 ...
written 8 weeks ago by Leonardo Collado Torres690
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Comment: C: how to download bigwig from recount2?
... ```R hms 0.5.0 2019-07-09 [1] CRAN (R 3.6.1) htmlTable 1.13.1 2019-01-07 [1] CRAN (R 3.6.1) htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.6.1) htmlwidgets 1.3 2018-09-30 [1] CRAN (R 3.6.1) httr 1.4.1 2019- ...
written 8 weeks ago by Leonardo Collado Torres690

Latest awards to Leonardo Collado Torres

Popular Question 3 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 10 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 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
Popular Question 17 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 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 2.3 years ago, created an answer that has been accepted. For A: Issue creating a genomic state object in derfinder from an Ensembl GTF file
Scholar 2.3 years ago, created an answer that has been accepted. For A: Number of IRanges elements in TCGA HiSeqV2 dataset
Scholar 2.3 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 2.3 years 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 2.3 years ago, created an answer that has been accepted. For A: derfinder: analyzeChr() breaks on chromosomes > 22
Scholar 2.3 years ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Popular Question 2.3 years 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 2.3 years 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 2.4 years ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
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Scholar 2.6 years ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Scholar 3.5 years ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
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Scholar 4.3 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
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Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: derfinder: fullCoverage() problems
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