User: Barry Digby

gravatar for Barry Digby
Barry Digby500
Reputation:
500
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Trusted
Location:
National University of Ireland, Galway
Twitter:
@BarryDigby
Last seen:
6 hours ago
Joined:
2 years, 4 months ago
Email:
b********@hotmail.com

PhD candidate @NUIG

Posts by Barry Digby

<prev • 97 results • page 1 of 10 • next >
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Circlize genomicLabel won't plot outside.
... Hi, I'm a beginner to using circlize and can't get past this issue where the `genomicLabels` will not plot to the outside of the circle. Here is a small example using 3 exons as the track. > x ID x y exon1 0 100 exon2 0 200 exon3 0 166 And the 3 miRs that bind t ...
circlize written 1 day ago by Barry Digby500
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Comment: C: How to select differential expressed genes using DeSeq2?
... You specifically want to evaluate genes with `NAs` in the wet lab? Don't. Try this filtering method, it should help prevent NA's and spurious (very high/negative Log2FC) calls showing up in your up/down regulated results: library(IHW) library(apeglm) res <- results(dds, filter ...
written 6 days ago by Barry Digby500
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Comment: C: How to select differential expressed genes using DeSeq2?
... Hi Aynur, The code I gave you filters by `pvalue`, not `padj`, it will return more genes. Furthermore, the code example you provided does not filter by `log2FoldChange` as expected (at least when i tested it). It only filters by `padj` which is a rather egregious error. If you want to replicate ...
written 6 days ago by Barry Digby500
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Answer: C: How to select differential expressed genes using DeSeq2?
... You can convert the `res` object to a dataframe by simply calling `res_df <- as.data.frame(res)`. Then apply filtering like these two functions do: get_upregulated <- function(df){ key <- intersect(rownames(df)[which(df$log2FoldChange>=1)], rownames(df)[which(df$pvalue< ...
written 7 days ago by Barry Digby500
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Answer: A: Generate BED12 file from genomic coordinates
... Try the script at the following location: https://github.com/BarryDigby/circrna/blob/master/bin/get_mature_seq.sh Must supply GTF file as first argument to script (gencode) Must have `unwanted_biotypes.txt` in same dir. Logic: |-- Checks circRNA for overlapping features in GTF file (protein ...
written 15 days ago by Barry Digby500
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Comment: C: Generate BED12 file from genomic coordinates
... I intend to, just need to test it at a larger scale tomorrow before doing that. ...
written 16 days ago by Barry Digby500
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Generate BED12 file from genomic coordinates
... Hi all, As the title suggests, is it possible to generate a `bed12` file given a genomic range? Here are some examples; Standard bed file: chr22 20564449 20566817 circrna 0 + I would like to generate a bed12 file from the underlying sequence that would ultimately result in: chr22 20 ...
bedtools bed12 ucsc written 17 days ago by Barry Digby500
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Comment: C: STAR index file for GRCH37
... I would drop the `--limitGenomeGenerateRAM` and `--outFileNamePrefix` flags You could reduce `--runThreadN` to say, 8, (it might be a resource issue with your cluster). Also make sure that the `--genomeDir` exists. Let me know how you get on ...
written 25 days ago by Barry Digby500
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Comment: C: DESeq2 analysis with high number of samples
... You will never know until you add all 200 samples, I would suggest doing that instead of dipping your toe in with small sample sizes. Judging by your 1st PCA plot, it is not surprising there are no DE genes, however maybe the other 160 samples will separate better on the PCA plot (: Have a read o ...
written 4 weeks ago by Barry Digby500
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Comment: C: TCGA- which files to download for analyzing differentially expressed miRNAs
... I have code here (https://github.com/BarryDigby/TCGA_Biolinks/blob/master/TCGA_Biolinks.Rmd) that does everything you want: download data, prepare metadata, filtering coding genes, differential expression analysis. It's a good basic template to start with. It was conducted on TCGA PRAD. Install pac ...
written 5 weeks ago by Barry Digby500

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