User: reilly.brian.m

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Posts by reilly.brian.m

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Plot association between genotype and splicing ratio using ggplot
... ggplot is designed to work on "long" format matrices such as you have used in your working example. Its much easier to just use a very large and "Redundant" long matrix than it is to try to do it using two separate matrices. Why are you concerned about redundancy?? I'm currently working on a table ...
written 4 months ago by reilly.brian.m60
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Comment: C: Best-suited unit of expression to perform between-sample comparison
... Could you not use DESeq2 to normalize the counts to library size before calculating the TPM to make it comparable across samples? ...
written 4 months ago by reilly.brian.m60
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Comment: C: Tool to predict Enhancer gene target
... Wow I'm not sure how I didn't try that before, but thank you for that quick and easy answer! ...
written 4 months ago by reilly.brian.m60
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Comment: C: Tool to predict Enhancer gene target
... Jared - I know this is late, but do you know where I can download the GeneHancer table? I see the track hub on UCSC, but I'd like to use the database itself for some analyses in R if possible, but I can't find a download anywhere? ...
written 4 months ago by reilly.brian.m60
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Comment: C: how to choose optimal K in Consensus clustering
... Are you aware of any studies that have validated the PAC as the most accurate K-estimating measure? I've seen countless studies proposing a new method for X which appear to show that the new method outperforms the old method, only for that study to be refuted in the future. Unless the PAC has be ...
written 17 months ago by reilly.brian.m60
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Comment: C: Is hierarchical clustering of significant genes 'supervised' or 'unsupervised' c
... Since you are using outside knowledge (differences between 2 known groups of samples) this would fall under supervised or semi-supervised clustering... However in a paper you could describe it as unsupervised clustering of differentially expressed genes and everyone would understand that it was semi ...
written 19 months ago by reilly.brian.m60
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Comment: C: Heatmaps in R
... I do it with ggplot2 and it is awful, but I like the flexibility it gives me with the layout. ...
written 2.6 years ago by reilly.brian.m60
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Comment: C: considerations for epiallele studies (DNA methylation Bisulfite Sequencing)
... I understand that it is difficult to find regions with > 4 contiguous CpGs, but I don't understand why they specifically exclude regions that DO have > 4 contiguous CpGs. I think it may have something to do with the statistic calculations having different biases for differnt length epialleles ...
written 3.1 years ago by reilly.brian.m60
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considerations for epiallele studies (DNA methylation Bisulfite Sequencing)
... I am doing a study of bisulfite sequencing data from a bunch of samples, and I'm interested in looking into epialleles, epipolymorphisms, and measures of DNA methylation disorder. One thing I keep seeing in papers is that every study seems to limit their analysis to only epialleles with 4CpGs, even ...
dna methylation bisulfite sequencing epiallele written 3.1 years ago by reilly.brian.m60 • updated 2.9 years ago by rkostadi60
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Comment: C: Hg19 regions for Intergenic, Promoters, Enhancer, Exon, Intron, 5-UTR, 3-UTR and
... This is great, I like the format you chose.   I am curious though, how did you define enhancers? ...
written 3.7 years ago by reilly.brian.m60

Latest awards to reilly.brian.m

Supporter 15 months ago, voted at least 25 times.
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Software to analyse mutations in sanger sequencing files
Student 2.9 years ago, asked a question with at least 3 up-votes. For considerations for epiallele studies (DNA methylation Bisulfite Sequencing)

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