User: Leonardo Collado Torres

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710
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Trusted
Location:
United States
Website:
http://lcolladotor.git...
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fellgernon
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Last seen:
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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 • 199 results • page 1 of 20 • next >
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Comment: C: how to download bigwig from recount2?
... This is a separate question, please post a new question Daniel. Thank you =) ...
written 8 days ago by Leonardo Collado Torres710
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Comment: C: recount TCGA data one gene_id mapped to multiple symbols and vice versa
... Then you need to look at resources outside of `recount`, say, ENSEMBL, to check which is the particular gene ID you want based on the gene structure. It's not rare for two Ensembl IDs to match to the same gene symbol. ...
written 5 weeks ago by Leonardo Collado Torres710
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Comment: C: recount TCGA data one gene_id mapped to multiple symbols and vice versa
... Thanks for this answer James! ...
written 5 weeks ago by Leonardo Collado Torres710
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Comment: C: recount TCGA data one gene_id mapped to multiple symbols and vice versa
... ## R 3.4.4 ```R > genes <- c('ENSG00000283638', 'ENSG00000015479', 'ENSG00000280987') > AnnotationDbi::mapIds(org.Hs.eg.db::org.Hs.eg.db, + genes, 'SYMBOL', 'ENSEMBL', + multiVals = 'CharacterList') 'select()' returned 1:1 mapping between keys and columns CharacterList of length 3 ...
written 5 weeks ago by Leonardo Collado Torres710
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Answer: A: recount TCGA data one gene_id mapped to multiple symbols and vice versa
... Hi Sheldon, The gene symbols in `recount` were obtained using this code https://github.com/leekgroup/recount/blob/master/R/reproduce_ranges.R#L95-L97 that relies on `AnnotationDbi::mapIds()` and `org.Hs.eg.db::org.Hs.eg.db`, which I adapted below for the case you report. ```R genes <- c('ENSG00 ...
written 5 weeks ago by Leonardo Collado Torres710
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Comment: C: Detection of large regions of expression
... Awesome, thanks for sharing the code! =) Best, Leo ...
written 11 weeks ago by Leonardo Collado Torres710
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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 11 weeks ago by Leonardo Collado Torres710
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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 12 weeks ago by Leonardo Collado Torres710
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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 3 months ago by Leonardo Collado Torres710
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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 3 months ago by Leonardo Collado Torres710

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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 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 13 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 19 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 19 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 2.5 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 2.5 years ago, created an answer that has been accepted. For A: Number of IRanges elements in TCGA HiSeqV2 dataset
Scholar 2.5 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 2.5 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 2.5 years ago, created an answer that has been accepted. For A: derfinder: analyzeChr() breaks on chromosomes > 22
Scholar 2.5 years ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Popular Question 2.5 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 2.5 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 2.5 years ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
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