User: b.d237
b.d237 • 140
- Reputation:
- 140
- Status:
- Trusted
- Location:
- National University of Ireland, Galway
- Last seen:
- 16 hours ago
- Joined:
- 1 year, 2 months ago
- Email:
- b********@hotmail.com
de novo viral miRNA discovery
Posts by b.d237
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2
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1
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135
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... Follow the detailed workflow here : https://github.com/twbattaglia/RNAseq-workflow :
# Add ENTREZ ID
results$entrez <- mapIds(x = org.Mm.eg.db,
keys = row.names(results),
column = "ENTREZID",
keytype = "SYMBOL",
...
written 7 days ago by
b.d237 • 140
0
votes
1
answer
142
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1
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... Many thanks Prakash!! ...
written 28 days ago by
b.d237 • 140
0
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1
answer
142
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1
answers
... Hi Ram,
Yes I am using R studio. To test that theory I placed
outfile="/Users/b/Desktop/Hallmarks_plots.pdf"
pdf(file=outfile)
..FOR LOOP..
dev.off()
To try and capture all plots in 1 pdf. The resulting pdf cannot be opened (is damaged). ...
written 28 days ago by
b.d237 • 140
6
votes
1
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142
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5 follow
1
answer
... Hi,
I have been using the package [fgsea][1], and I would like to use a for loop in R to output multiple Enrichment plots.
So far I can generate a plot of the desired pathway using:
plotEnrichment(pathway =
pathways.hallmark[["HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION"]],
gseaPar ...
1
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2
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6.1k
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2
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... Try row.names = TRUE.
Also, you want to use col.names = FALSE, as GSEA complains when 'Gene' and 'metric' are in the rnk. file. ...
written 5 weeks ago by
b.d237 • 140
1
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2
answers
6.1k
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2
answers
... **`.....`**
filtered <- na.omit(y)
write.table(filtered ,file="DE_genes.rnk",quote=F,sep="\t",row.names=F)
...
written 5 weeks ago by
b.d237 • 140
0
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0
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315
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... Yeah I think I had gone too far,
design = ~ condition + celltype + condition:celltype
Is not what I was after. Leaving out condition:celltype allowed me to control for the effects of condition. My phrasing was unclear -- instead of 'across condition', I should have said controlling for condit ...
written 10 weeks ago by
b.d237 • 140
1
vote
0
answers
315
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0
answers
... Hi,
I am attempting to compare the following samples in DESEQ2 that follow and experimental design of:
condition celltype
Ctrl A
Ctrl B
Ctrl C
Ctrl D
CYTO A
CYTO B
CYTO C
CYTO D
(Replica ...
0
votes
1
answer
758
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1
answers
Comment:
C: GATK Panel Of Normals (PoN)
... The error output tells you what the problem is. -v is not a recognized option. You probably want to use -V instead of -vcfs
Uppercase, not lower case. ...
written 3 months ago by
b.d237 • 140
0
votes
1
answer
386
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1
answers
... Contacted the developer Adam Grundhoff, its available here:
[VMir Analyzer][1]
[1]: http://virus-genomics.org/software/vmir/vmir.html ...
written 4 months ago by
b.d237 • 140
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