Admin: Marcel Ramos

gravatar for Marcel Ramos
Marcel Ramos ♦♦ 60
Reputation:
60
Status:
Trusted
Location:
United States
Last seen:
3 days, 6 hours ago
Joined:
2 years, 7 months ago
Email:
m****************@roswellpark.org

Posts by Marcel Ramos

<prev • 18 results • page 2 of 2 • next >
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Answer: A: PWM with columns that add up to 1
... Hi clausdkuhn,  Please see ?Biostrings::matchPWM for more details.    Regards, Marcel  ...
written 10 months ago by Marcel Ramos ♦♦ 60
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Answer: A: BiocCheck incorrectly reports I'm not registered on this site
... It looks like you're registered. This shouldn't be an error. Have you updated your BiocCheck?  https://support.bioconductor.org/api/email/david.a.quigley%40gmail.com/   ...
written 11 months ago by Marcel Ramos ♦♦ 60
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Answer: A: Classes and methods for working with segmented copy number data
... Hi Sean! We have the `MultiAssayExperiment::RangedRaggedAssay` class that can handle all of the above. It would require you to have a `GRangesList` object with a "score" metadata column denoting copy_number. The `GRangesList` can be created from a `DataFrame` using the `GenomicRanges::makeGRangesL ...
written 13 months ago by Marcel Ramos ♦♦ 60
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Comment: C: TCGAbiolinks 403 Forbidden Error
... Core team member Valerie pointed out that this error was missed because of numerous \dontrun flags that were used in the documentation. Particularly in the TCGAquery_maf.Rd file (pertinent to this issue, but there are more).  It is good to have tests so that when something goes wrong, it is easily ...
written 15 months ago by Marcel Ramos ♦♦ 60
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TCGAbiolinks 403 Forbidden Error
... Hello everyone,  I am posting this issue for the `TCGAbiolinks` package because I'm trying to download data but it seems like the link it uses is now broken.  https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/ The code that I ran encountering this '403 Forbidden Err ...
bug tcgabiolinks issue written 15 months ago by Marcel Ramos ♦♦ 60 • updated 14 months ago by tiagochst80
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Answer: A: Downloading bt.exon_quantification with TCGAbiolinks
... Hi Tiago,  Thank you for your prompt response. Yes, the directory was created. It seems like the issue has to do with tilde expansion.  Compare:  TCGAdownload(prad, "~/Documents/rawdata/", type = "bt.exon_quantification") TCGAdownload(prad, "/home/mr148/Documents/rawdata/", type = "bt.exon_qua ...
written 17 months ago by Marcel Ramos ♦♦ 60
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Downloading bt.exon_quantification with TCGAbiolinks
... Hi there, I am trying to download the "bt.exon_quantification" files using TCGAbiolinks but I'm running into a bug: library(TCGAbiolinks) prad <- TCGAquery(tumor = "prad", platform = "IlluminaHiSeq_RNASeqV2", level = 3) TCGAdownload(prad, "~/Documents/rawdata/", type = "bt.exon_quantification" ...
bug tcgabiolinks written 17 months ago by Marcel Ramos ♦♦ 60
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Downloading Thymoma data (THYM)
... Hi there, I'm trying to download the Thymoma data from TCGAbiolinks::TCGAquery_maf but I am unable to because I get an error: thym <- TCGAquery_maf(tumor = "thym") Error in df$Deploy.Status : $ operator is invalid for atomic vectors  Traceback:  3 subset.default(df, df$Deploy.Status == "Avai ...
bug tcgabiolinks written 18 months ago by Marcel Ramos ♦♦ 60

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Scholar 5 months ago, created an answer that has been accepted. For A: Classes and methods for working with segmented copy number data
Scholar 5 months ago, created an answer that has been accepted. For A: Classes and methods for working with segmented copy number data

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