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Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 5 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
Dario Strbenac
★ 1.5k
3
votes
3
replies
397
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 5 weeks ago by
alan.ocallaghan
▴ 160 • written 5 weeks ago by
Najla Abassi
• 0
3
votes
3
replies
369
views
plotUMAP Gene Set Faceted
scater
updated 3 months ago by
alan.ocallaghan
▴ 160 • written 3 months ago by
Dario Strbenac
★ 1.5k
1
vote
1
reply
248
views
plotUMAP and ggplotly Cell IDs Display
scater
updated 3 months ago by
alan.ocallaghan
▴ 160 • written 3 months ago by
Dario Strbenac
★ 1.5k
1
vote
7
replies
6.6k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP
scater
Matrix
updated 9 weeks ago by
Hervé Pagès
16k • written 5 months ago by
inzirio
▴ 10
0
votes
3
replies
1.1k
views
Is logNormCounts log2 normalised counts as default?
scuttle
scater
updated 8 months ago by
ATpoint
★ 4.1k • written 8 months ago by
Abbi Edwards
• 0
0
votes
6
replies
873
views
plotHeatmap annotation error
plotHeatmap
scater
10 months ago
Alina
• 0
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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…
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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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