User: Leonardo Collado Torres

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http://lcolladotor.git...
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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 • 183 results • page 1 of 19 • next >
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Comment: C: scale_counts targetSize normalization for recount2 counts
... ## Definitions We have `scale_counts(current_bp_counts)` = `current_bp_counts` * (`target_AUC` / `current_AUC` ) / `avg_target_read_Length` = `current_bp_counts` * `targetSize` / `current_AUC` and `read_counts(current_bp_counts)` =`current_bp_counts` / `avg_observed_read_length` = `current_bp_ ...
written 5 days ago by Leonardo Collado Torres640
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Comment: C: scale_counts targetSize normalization for recount2 counts
... Hi again, ## (1) No. Say that we have two samples, one with 45 million reads with an average mapped length of 75 base-pairs. The sum of the total coverage (AUC) for sample 1 is 45 mi * 75 = 3,375 x 10^6 For sample 2, we have 40 million reads with an average mapped length of 80 base-pairs, so sampl ...
written 6 days ago by Leonardo Collado Torres640
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Answer: A: scale_counts targetSize normalization for recount2 counts
... Hi, For normalizing the coverage and visualizing the base-pair level data as in Figure 1 (top row) of https://f1000research.com/articles/6-1558/v1, we scale the data to the same number of reads (of the same length). In this case it matters that the AUC is the same for each sample after scaling, so ...
written 8 days ago by Leonardo Collado Torres640
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Comment: C: Recount data for unannotated genes
... Thanks for posting this answer Chris! Best, Leo ...
written 9 weeks ago by Leonardo Collado Torres640
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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 10 weeks ago by Leonardo Collado Torres640
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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 10 weeks ago by Leonardo Collado Torres640
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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 6 months ago by Leonardo Collado Torres640
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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 6 months ago by Leonardo Collado Torres640 • updated 6 months ago by Martin Morgan ♦♦ 23k
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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 7 months ago by Leonardo Collado Torres640
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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 8 months ago by Leonardo Collado Torres640

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Popular Question 7 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 Getting a flat metadata table from the XML files in TCGA: is it feasible?
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
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