User: bimlay2

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bimlay230
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Posts by bimlay2

<prev • 8 results • page 1 of 1 • next >
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Do all samples in SRA have a corresponding sample in BioSample?
... I would like to depend on Biosample database for sample metadata rather than SRA. Do all SRA samples have a corresponding sample in Biosample? I've browsed a handful of studies, and found that they do. However, I'm wondering if anyone knows better than I. ...
sra sequencing written 26 days ago by bimlay230 • updated 26 days ago by JJ470
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Comment: C: How many runs, samples, and studies are in the Sequence Read Archive?
... Perfect, thanks for this! ...
written 5 weeks ago by bimlay230
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How many runs, samples, and studies are in the Sequence Read Archive?
... I have the following numbers, but I can't figure out where I found them. I can't find them again, and it's driving me crazy! Thanks for your help! Studies: 210832 Samples: 6322688 Runs: 7675139 ...
sequencing written 5 weeks ago by bimlay230 • updated 5 weeks ago by jared.andrews073.9k
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Comment: C: SRA Run Collector Google Sheets Add-on: Looking for feedback!
... Permissions as in permissions from Google. The script uses a URL fetch method to get information from NCBI. Google will request permission to do this before you can run the script. This is not a command line tool. There are no real client permissions involved. ...
written 4 months ago by bimlay230
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Comment: C: SRA Run Collector Google Sheets Add-on: Looking for feedback!
... Yes, I've seen this tool. My inspiration for this project is that I wanted to know sample attributes and various other metadata fields for the associated runs. The desired output of my tool is not necessarily run numbers alone, which are easy to get from sra-explorer. Rather, my tool collects run i ...
written 4 months ago by bimlay230
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Tool: SRA Run Collector Google Sheets Add-on: Looking for feedback!
... I recently put together a simple Google App Script add-on for sheets that retrieves run information from SRA from a GSE, SRP, or PRJNA accession. The git repository can be found [here][1]. All of the code can be found in the Code.gs file. SRA provides its metadata in XML format, but if you want to ...
tool rna-seq written 4 months ago by bimlay230
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Comment: C: Identifying genes associated with a binary classification for many cell lines
... Thanks for your comment. I actually used DESeq2 to generate DE results. The mean-dispersion trend looked weird, and I got super, super low p-values. I wasn't sure if any DE method was suited for 35 cell lines lumped into two groups. ...
written 8 months ago by bimlay230
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Identifying genes associated with a binary classification for many cell lines
... I have gene-wise expression data for 35 cell lines with ~3 runs per cell line. I also have a binary classification for each cell line associated with a biological phenomenon. I am interested in finding the genes that are most associated with the binary classification. I have tested several approach ...
R rna-seq written 8 months ago by bimlay230

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