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scuttle
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Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 7 months ago by
ATpoint
★ 4.5k • written 7 months ago by
Dario Strbenac
★ 1.5k
0
votes
3
replies
1.5k
views
Is logNormCounts log2 normalised counts as default?
scuttle
scater
updated 14 months ago by
ATpoint
★ 4.5k • written 14 months ago by
Abbi Edwards
• 0
1
vote
0
replies
1.8k
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Convert SpatialExperiment Object to Seurat Object
scuttle
scater
seurat
SpatialExperiment
21 months ago
cathalgking
▴ 10
0
votes
1
reply
915
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cell_count column in SpatialExperiment Object
scuttle
scater
SpatialExperiment
updated 21 months ago by
alan.ocallaghan
▴ 160 • written 22 months ago by
cathalgking
▴ 10
2
votes
2
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1.5k
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scuttle:: librarySizeFactors returning non-finite values
normalizeCounts
scran
librarySizeFactors
scuttle
scRNAseq
2.7 years ago
behr201
• 0
3
votes
3
replies
2.0k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater
SingleCellExperiment
BiocParallel
scuttle
scran
3.0 years ago
enricoferrero
▴ 660
4
votes
5
replies
2.8k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran
SingleCellExperiment
scuttle
scater
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
enricoferrero
▴ 660
5
votes
4
replies
6.9k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran
scater
scuttle
updated 4.3 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
enricoferrero
▴ 660
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Comment: How many of my genes from my gene list are in each KEGG pathway?
by
josephasmith1310
• 0
> You can compare the number in the column setSize versus the number of > genes in core_enrichment. The former corresponds to the number of…
Comment: EuroBioC2024 abstract submission is open!
by
Esperan
• 0
Great information about the EuroBioC2024 conference! https://openreview.net/group?id=bioconductor.org/EuroBioC/2024/Conferences [slope](htt…
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
by
Gordon Smyth
51k
I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…
Comment: Adjusted p-values become NA when sub-setting samples
by
txema.heredia
• 0
Thanks! I've been looking into DESeq2's code and, indeed, I get matching results when running manually the code inherited from the `genefi…
Answer: DESeq2 interaction between cancer cells and microenvironment cells
by
Michael Love
42k
I don't really know what you mean by "come from the contamination". You can look at the main effects and the interaction, but I don't know …
Votes
Answer: How do I merge a list of GRanges?
A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
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