User: ldyer2006

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ldyer200630
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Posts by ldyer2006

<prev • 12 results • page 1 of 2 • next >
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Comment: C: ATACseqQC - Cut-site probability greater than 1?
... Thanks a lot, that is very helpful. ...
written 9 months ago by ldyer200630
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ATACseqQC - Cut-site probability greater than 1?
... Hi guys, I was just wondering if anybody here had any experience working with the ATACseqQC R package? The package seems to function well for me over all, and gives reasonable results when I apply it to the entire mouse genome (Using the following command): sigs.Irx3.0 <- factorFootprints( ...
atac-seq atacseqqc written 9 months ago by ldyer200630 • updated 9 days ago by Lizzy0
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Validating a mouse model with RNA-Seq
... Hi folks, I've recently started a new job in a new country and one of my first tasks is going to be to validate a mouse cell model (ME3), primarily using RNA-Seq. We're working with adipocyte differentiation, and we've run a time-course RNA-Seq of the differentiation procedure (About 7 days). I have ...
rna-seq written 14 months ago by ldyer200630 • updated 12 months ago by Biostar ♦♦ 20
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Comment: C: WGCNA and VisAnt
... Yes, when you put it like that, it makes much more sense. I have since re-run the analysis and now that I've looked more into it after these posts, I think I have a slightly better handle on it and the networks are at least beginning to look like networks. I think, with a lot more fiddling and a lot ...
written 14 months ago by ldyer200630
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Comment: C: WGCNA and VisAnt
... Thanks, Jacob. That is somewhat re-assuring. Selecting the layout -> relaxing option seems to generate a plot that is slightly more like what I was expecting, thank you. But is it really acceptable that *all* of my gene network measures fall within such a tight range? VisAnt allows me to set we ...
written 14 months ago by ldyer200630
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Comment: C: WGCNA and VisAnt
... It was low, just around 0.02, to ensure that I was seeing all of the connections as I just chose 25 hub genes. ...
written 14 months ago by ldyer200630
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WGCNA and VisAnt
... Hello folks, I'm hoping that you can help me understand some of the results I'm getting from WGCNA when it comes to visualising a network. I have managed to extract my modules from the data set, and graphed them against their trait data, and now I'm looking to produce a visualisation of the gene ne ...
rna-seq written 14 months ago by ldyer200630 • updated 14 months ago by Jake Warner670
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Confusion regarding WGCNA
... Hi folks, I'm currently attempting some time-course analysis of a recent RNA-Seq run using WGCNA. I have 5 time points, with 4 biological replicates of 2 conditions at each point, so around 40 samples total. The main problem that I'm having is simply one of confusion. I'm not sure exactly how to inc ...
rna-seq written 14 months ago by ldyer200630 • updated 14 months ago by Jake Warner670
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Comment: C: Counting k-mers in a multifasta file
... Hi! I actually found a very useful script that does what I want, although it's going to take a while: https://noble.gs.washington.edu/proj/nucsvm/fasta2matrix.py Pre-splitting the data was definitely a poor decision..!! ...
written 20 months ago by ldyer200630
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Comment: C: Counting k-mers in a multifasta file
... Hi! I actually found a very useful script that does what I want, although it's going to take a while: https://noble.gs.washington.edu/proj/nucsvm/fasta2matrix.py My sequence file is just the result of a bedtools getfastafrombed command on my chosen ChIP-Seq dataset using hg18 as the reference geno ...
written 20 months ago by ldyer200630

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Popular Question 18 months ago, created a question with more than 1,000 views. For Calling differential peaks on ATAC-seq data

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