User: gkuffel

gravatar for gkuffel
gkuffel10
Reputation:
10
Status:
New User
Location:
Loyola University
Last seen:
1 month, 3 weeks ago
Joined:
8 months ago
Email:
g******@luc.edu

I manage the Loyola Genomics Facility. A core that provides experimental design, library preparation, next generation sequencing, and bioinformatics to a broad user base.

Posts by gkuffel

<prev • 7 results • page 1 of 1 • next >
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Comment: C: DESeq2 Design Formula for Time Series Experiment
...   David, Thank you so much for your reply. I have a few more questions if you have time: 1. So with my current design (design =~ Timepoint + Patient) am I testing for differences between patients while controlling for variability caused by time? 2.  If I use the design: design = ~ Timepoint + Tr ...
written 11 weeks ago by gkuffel10
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DESeq2 Design Formula for Time Series Experiment
... Hi everyone, I have miRNA-Seq data for an experiment with the following parameters: SampleID     Treatment     Timepoint     Patient    P1_0                  TB                 0             1    P1_1                  TB                 1             1    P1_2                  TB               ...
deseq2 written 12 weeks ago by gkuffel10 • updated 12 weeks ago by David Requena20
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Comment: C: Sample not clustering as expected in DESeq2
... Thanks for your input Michael. ...
written 5 months ago by gkuffel10
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Answer: A: Sample not clustering as expected in DESeq2
... Thanks for your input Michael. ...
written 5 months ago by gkuffel10
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Sample not clustering as expected in DESeq2
... Hoping I can get some help. I have been using DESeq2 for several months now on several different projects (I manage a NGS core). For most of these projects, the samples do not cluster as I would expect. For example, not all of the treatments will cluster with the treament group and not all of the co ...
deseq2 euclidean sample distance written 6 months ago by gkuffel10
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Comment: A: Running DESeq2 inside local Galaxy instance
... Thanks, I was trying to get some input from the author of the tool, Michael Love and thought this forum would be the best place to reach him. ...
written 8 months ago by gkuffel10
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Running DESeq2 inside local Galaxy instance
... Hi everyone,   We have tried many times to install DESeq2 to our local instance of Galaxy. The install is successful but when we run the tool we get the following error:   Fatal error: An undefined error occurred, please check your input carefully and contact your administrator. Error in librar ...
deseq2 galaxy written 8 months ago by gkuffel10

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