User: dodausp

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dodausp110
Reputation:
110
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Trusted
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Denmark/Copenhagen/BRIC
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3 days, 5 hours ago
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3 years, 4 months ago
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Posts by dodausp

<prev • 19 results • page 1 of 2 • next >
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How to find true mutations in tumor by removing the background from matched sample?
... **In other words, How to normalize tumor SNPs by using matched sample??** . Hi, everyone! So, I have a dataset of somatic mutations consisting of 3 samples for each individual, that being: blood, primary tumor and recurrent tumor. I would like to take advantage of the blood samples and use it as ...
normalization exome-seq R snp pipeline written 3 months ago by dodausp110 • updated 3 months ago by bernatgel1.8k
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Answer: A: Data retrieval icgc
... I am not sure if it is still a topic that people come after, or if the ICGC portal has been updated after the last thread here. However, I did come across your question, @anshupa.vssut, when looking exactly for a way to retrieve the data from ICGC. So, for those who don't mind downloading the data ...
written 3 months ago by dodausp110
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Answer: A: Drug interaction not running in MAFtools
... Problem solved! There is no logic behind it, really. But it worked. Well, simply get it directlly from GitHub: devtools::install_github('PoisonAlien/maftools') I have tried that on the day I posted the issue here, but didn't work. I did that again today, and it worked. :| In any case, the au ...
written 3 months ago by dodausp110
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Comment: C: Drug interaction not running in MAFtools
... Hi, @zx8754 It is indeed. I saw you were also there. So, thank you for the support. The reason why is also here is because I posted the issue first here, and a day later on GitHub, to the author. But the problem seems to be solved. I will post here shortly. Thanks again for the follow-up. ...
written 3 months ago by dodausp110
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Drug interaction not running in MAFtools
... Hi! I am trying to run the `drugInteractions` function in the MAFtools pipeline, but it seems that it is simply not there. Here is the message I am getting: > library("maftools") > druggable = drugInteractions(maf = STES_maf, fontSize = 0.75) Error in drugInteractions(maf = laml, ...
R maftools exome-seq snp written 3 months ago by dodausp110
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Comment: C: Retrieving miRNA data from Firehose by using RTCGAToolbox
... I just performed the same lines as above. Although the message error was still there, the file was successfully exported to the home directory. So, this should do: > miOV <- getFirehoseData(dataset="OV", runDate = "20160128", gistic2Date = NULL, clinical = TRUE, miRNAArray = T, forceDown ...
written 3 months ago by dodausp110
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Answer: A: Retrieving miRNA data from Firehose by using RTCGAToolbox
... Case solved! Although it still gives an error message after performing the getData function, it still exports the data. ...
written 3 months ago by dodausp110
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Retrieving miRNA data from Firehose by using RTCGAToolbox
... Hi, everyone! Is there anyone here familiar with or using the RTCGAToolbox package? I found it to be very useful when importing, compiling and exporting data from the Firehose repository. However, I am simply unable to export miRNA data. Here is what I'm doing: > miOV <- getFirehoseData(d ...
firehose mirna rtcgatoolbox R written 3 months ago by dodausp110 • updated 3 months ago by zx87546.8k
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Comment: C: Adding unique index or names to merged data frames
... Thanks a lot, benformatics! It was extremely helpful! Amazing! ...
written 3 months ago by dodausp110
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Adding unique index or names to merged data frames
... Hi everyone, I am pretty sure most of you can come with a quick solution to that, so sorry for the simple question. Here is the issue, I have multiple files for SNV counts, each corresponding to a sample. I want to merge all into one data frame, but still would like to keep a unique ID for each fil ...
merge tcga index snp sequencing written 3 months ago by dodausp110 • updated 3 months ago by benformatics640

Latest awards to dodausp

Popular Question 9 weeks ago, created a question with more than 1,000 views. For How to set the control group in microarray analysis from illumina data?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Drug interaction not running in MAFtools
Scholar 3 months ago, created an answer that has been accepted. For A: Retrieving miRNA data from Firehose by using RTCGAToolbox
Scholar 3 months ago, created an answer that has been accepted. For A: Retrieving miRNA data from Firehose by using RTCGAToolbox
Popular Question 5 months ago, created a question with more than 1,000 views. For Biobase not running in R 3.5.0

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