User: Leonardo Collado Torres

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Location:
United States
Website:
http://lcolladotor.git...
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fellgernon
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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 • 186 results • page 1 of 19 • next >
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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 2 days ago by Leonardo Collado Torres640
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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 2 days ago by Leonardo Collado Torres640
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Answer: A: how to download bigwig from recount2?
... Hi hyp15, You can download the BigWig files for a study using `download_study(project, type = "samples" )`. Note that `"samples"` is quoted, unlike the one you provided in your code above. So for example this works for downloading all the BigWig sample files for study SRP009615 (took 2 minutes for ...
written 2 days ago by Leonardo Collado Torres640
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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 8 weeks 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 8 weeks 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 weeks 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 4 months 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 4 months 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 4 months 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 8 months ago by Leonardo Collado Torres640

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Popular Question 8 weeks 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 8 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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Popular Question 15 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?
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