User: Barry Digby
Barry Digby • 630
- Reputation:
- 630
- Status:
- Trusted
- Location:
- National University of Ireland, Galway
- Twitter:
- @BarryDigby
- Last seen:
- an hour ago
- Joined:
- 2 years, 7 months ago
- Email:
- b********@hotmail.com
PhD candidate @NUIG
Posts by Barry Digby
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... good spot, hasn't been updated since 2016! ...
written 2 days ago by
Barry Digby • 630
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... The guide fails to mention the resources directory is on github which from experience, took a bit of extra digging around than was necessary.
It's here: https://github.com/BioInfoTools/BBMap/blob/master/resources/adapters.fa ...
written 2 days ago by
Barry Digby • 630
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... My bad, I'm used to biomaRt df's derived from count rownames. Feel free to change yours to an answer and ill remove mine. . ...
written 11 days ago by
Barry Digby • 630
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... Yep you're pretty much there.
Assuming `counts` is your counts matrix containing all samples, something to the effect of:
```
subset <- counts[which(rownames(counts) != biomart_list$Gene),]
```
edit: `!=` must be dataframes of equal length ...
written 14 days ago by
Barry Digby • 630
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Comment:
C: How to plot GSEA result?
... Some chump deleted my github accounts. I only recovered my primary account so that workflow is no longer available.
Follow this for `fgsea` - https://stephenturner.github.io/deseq-to-fgsea/#using_the_fgsea_package
And this for `GSEA` - https://www.biostars.org/p/238541/ ...
written 24 days ago by
Barry Digby • 630
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... If you edit it accordingly, yes. ...
written 24 days ago by
Barry Digby • 630
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... Try combining command 1 and 3, run command 2 first:
bowtie-build genome/GRCh38.fa GRCh38_idx
mapper.pl ../RawData.fq -e -h -i -j -k TGGAATTCTCGGGTGCCAAGG -l 18 -m -p GRCh38_idx -s reads_collapsed.fa -t reads_vs_genome.arf -v
Does bowtie make correct indices from a fa.gz file? Maybe y ...
written 5 weeks ago by
Barry Digby • 630
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1
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... This gets asked a lot. Should probably make a tutorial..
Switch `TCGA-PRAD` to `TCGA-BRCA` and don't blindly run the metadata section.
---
title: "TCGA_analysis"
author: "Barry"
date: "07/07/2020"
output: html_document
---
```{r setup, include=FALSE}
knitr::o ...
written 7 weeks ago by
Barry Digby • 630
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... If you want to control for the effect of Replicates, shouldn't the design be `~ replicate + condition`?
I am basing this on the following [workflow][1] from Mike Love et al.
> The simplest design formula for differential expression would be `~
> condition`, where condition is a column in co ...
written 8 weeks ago by
Barry Digby • 630
3
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1
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Answer:
C: HT-Seq count data coding gene
... This is what Hamid Ghaedi is referring to:
## filter for protein coding genes in matrix (currently > 50,000 rows)
mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
mrna_attributes <- getBM(attributes=c("external_gene_name",
...
written 10 weeks ago by
Barry Digby • 630
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For A: mireap procedure short tutorial
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