User: breckuh

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breckuh20
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Posts by breckuh

<prev • 12 results • page 1 of 2 • next >
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Answer: A: GWAS analysis tool
... I would recommend the book "Genome-Wide Association Studies and Genomic Predictions". It was published in 2013, so I thought it might be outdated given the newness and pace of the GWAS field, but I've found many of the chapters to be highly relevant, and they have saved me a lot of time with my firs ...
written 3 months ago by breckuh20
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Comment: C: Finding and downloading many Gene Expression Matrices from GEO?
... Thanks Kevin! What I found was that for single cell experiments, the common practice was to store the matrices in the supplementary files section of a GSE entry. I was able to download and extract many thousands of matrices. More cleaning and careful mapping work to do, but looking forward to gettin ...
written 4 months ago by breckuh20
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Comment: C: How much shorter is the short arm of a chromosome? And why?
... Thanks! Posted on SE. I didn't quite catch the fact that Biostars was purely focused on bioinformatics. Thanks for the guidance! ...
written 4 months ago by breckuh20
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Comment: A: RNA-seq data from human tumors in mice (PDTX)
... Would single cell RNAseq solve this? You could more reliably identify which cells come from the tumors versus the mice and then proceed with your transcriptome analysis. ...
written 4 months ago by breckuh20
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Comment: C: creating ped file from txt file
... Did you ever solve this? I have a "txt" file in the same format and am having trouble figuring out a column: https://www.biostars.org/p/343493/ ...
written 4 months ago by breckuh20
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What does SNP mean in data from an Illumina MetaboChip final report?
... I am analyzing some data from 2015 and the original postdoc has moved on. The file is named "072312_FinalReport.txt" and has ~197k SNP measurements for 60 people. I have figured out the meaning of all of the columns, except for the last column. Can someone explain what "SNP" in the last column ([T/ ...
snp written 4 months ago by breckuh20
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(Closed) How much shorter is the short arm of a chromosome? And why?
... I keep reading that the p arm is shorter than the q arm. But I cannot find an explanation of how much shorter nor an explanation for the difference. ...
genome written 4 months ago by breckuh20
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Comment: C: If I downloaded all of the data accessible from NCBI's FTP site, how much space
... Thanks! Looks like SRA is about 8.7 Petabytes: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi? ...
written 5 months ago by breckuh20
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Finding and downloading many Gene Expression Matrices from GEO?
... We are setting up a pipeline that takes in single cell Gene Expression Matrices, runs them through a series of various preprocessing steps, and then trains various machine learning models to generate classifiers for label(s) on those datasets. We'd like to build a collection of 1k datasets to test ...
next-gen rna-seq written 5 months ago by breckuh20 • updated 4 months ago by RamRS20k
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Comment: C: If I downloaded all of the data accessible from NCBI's FTP site, how much space
... I was thinking of doing something like that. I know they don't support SFTP. I haven't done any FTP crawling before but I imagine it's straightforward. I don't know how feasible it is. If there were 1B folders and I did 1k requests a second, it would take 10 days. Perhaps there are a few simple com ...
written 5 months ago by breckuh20

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