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glimma
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Glimma Interactive plots for RNAseq
Glimma
R markdown
rnaseq
6.2 years ago
Aurora
▴ 20
0
votes
1
reply
832
views
Why does the Glimma package require R >= 3.4.0 ?
glimma
updated 6.2 years ago by
Shian Su
▴ 40 • written 6.2 years ago by
gil.hornung
• 0
1
vote
3
replies
1.5k
views
problem installing the Glimma package
glimma
6.1 years ago
omran.allatif
• 0
2
votes
2
replies
1.0k
views
What to do when a bug is found in a BioConductor package (Glimma)
glimma
software error
updated 4.7 years ago by
Gordon Smyth
50k • written 4.7 years ago by
Sam
▴ 10
7
votes
6
replies
1.4k
views
BiocStyle::html_document does not render Glimma plots
Glimma
BiocStyle
updated 21 months ago by
Mike Smith
★ 6.5k • written 21 months ago by
neilzhao
▴ 30
1
vote
1
reply
491
views
Extracting the tophits from limma Volcanoplot and issue with geneIDs
limma
edgeR
Glimma
updated 16 months ago by
Gordon Smyth
50k • written 16 months ago by
Mohammad
• 0
1
vote
2
replies
1.0k
views
bug in Glimma - anno can't have T/F
Glimma
7.9 years ago
Jenny Drnevich
★ 2.0k
0
votes
2
replies
931
views
glimmaMA() produces blank plot if have annot column named "gene"
Glimma
updated 2.2 years ago by
Shian Su
▴ 40 • written 2.9 years ago by
Jenny Drnevich
★ 2.0k
0
votes
0
replies
1.1k
views
Glimma: Error: Length of groups must be equal to the number of columns in counts
Glimma
RNASeq
2.3 years ago
Jonas
• 0
0
votes
0
replies
527
views
Complex design in DESeq2 doesn't seem to be supported in Glimma
limma
Glimma
RNASeq
DESeq2
2.3 years ago
Jonas
• 0
10 results • Page
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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