User: osieman52

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osieman5210
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Posts by osieman52

<prev • 20 results • page 1 of 2 • next >
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Getting information about samples(.CEL files) from GEO using R
... Hello all, Using the `GEOquery` library in R I have managed to download 850 samples I am interested in. I used the following code for this: `x <- as.list(scan("fileWithGEOsampleAccesionCodes.txt", what ="" , sep = "" ))` `data= lapply(x,getGEOSuppFiles)` I have read the CEL files into an a ...
R micro-array written 2 days ago by osieman5210 • updated 1 day ago by Kevin Blighe13k
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Comment: C: Downloading multiple samples with GEO accesion numbers
... A small question added to this quetions, how would one find the batch IDs of the downloaded files? I want to create vectors in orderer to do this I need batch ids. How could I find or generate these batch ids ? ...
written 7 days ago by osieman5210
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Answer: A: Downloading multiple samples with GEO accesion numbers
... **Solution in R:** `library(GEOquery)` `x <- as.list(scan("files_with_GEO_accesionCodes.txt", what ="" , sep = "" ))` `files = lapply(x, getGEOSuppFiles)` ...
written 8 days ago by osieman5210
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Comment: C: Downloading multiple samples with GEO accesion numbers
... I managed to find an easy way to download the files I need by using R. library(GEOquery) x <- as.list(scan("files_with_GEO_accesionCodes", what ="" , sep = "" )) files = lapply(x, getGEOSuppFiles) Thank you for the responds! ...
written 8 days ago by osieman5210
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Comment: C: Downloading multiple samples with GEO accesion numbers
... Thanks for the link but, unfortunately this doesn't provide enough information to help me out. ...
written 8 days ago by osieman5210
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Downloading multiple samples with GEO accesion numbers
... Dear all, I have GEO accession numbers for 850 samples I would like to download. What is the easiest way to download a bulk of data from GEO database. I know that it can be done with a ftp or by using R (geoQuery). But I'am not sure how. Can someone please help me or give me advice on how to do ...
geo microarray written 8 days ago by osieman5210
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Comment: C: Average size and amount of Enhancer and Promoters ?
... In the data sets I have been using, I found significant differences in bp size of promoters (as well for enhancers). The biggest promoter I found had size of 2304635bp ,seems like a little but to much? ...
written 9 weeks ago by osieman5210
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Comment: C: Average size and amount of Enhancer and Promoters ?
... I have read this paper a while ago , didn't find what I was looking for specifically ,but it helped me with some additional info. thank you! ...
written 9 weeks ago by osieman5210
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Average size and amount of Enhancer and Promoters ?
... Hi, Is there any known literature about the average size(in bp) and amount(#count) of Enhancers and Promoters the genome has? I want to use this info in order to say something about the chance that a mutation can occur on these elements. (not based on conservation) Since I have my own data set an ...
genome dna written 10 weeks ago by osieman5210 • updated 10 weeks ago by natasha.sernova2.8k
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Comment: A: Bed tools for comparing files and calculating the percentage of different parts
... I think i made a mistake by saying that i wanted to use the combinations of these files as a whole. Since I think I should map my files against the whole human genome in order to say something about the chance that a mutations can occur in the files i use? pls correct me if i am wrong! ...
written 10 weeks ago by osieman5210

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Scholar 8 days ago, created an answer that has been accepted. For A: Downloading multiple samples with GEO accesion numbers

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