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scuttle
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2
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5
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560
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scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
scuttle
updated 4 days ago by
Aaron Lun
★ 28k • written 6 days ago by
Adam
▴ 10
2
votes
1
reply
545
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 8 months ago by
ATpoint
★ 4.6k • written 8 months ago by
Dario Strbenac
★ 1.5k
0
votes
3
replies
1.6k
views
Is logNormCounts log2 normalised counts as default?
scuttle
scater
updated 15 months ago by
ATpoint
★ 4.6k • written 15 months ago by
Abbi Edwards
• 0
1
vote
0
replies
1.9k
views
Convert SpatialExperiment Object to Seurat Object
scuttle
scater
seurat
SpatialExperiment
22 months ago
cathalgking
▴ 10
0
votes
1
reply
939
views
cell_count column in SpatialExperiment Object
scuttle
scater
SpatialExperiment
updated 22 months ago by
alan.ocallaghan
▴ 160 • written 23 months ago by
cathalgking
▴ 10
2
votes
2
replies
1.6k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts
scran
librarySizeFactors
scuttle
scRNAseq
2.8 years ago
behr201
• 0
3
votes
3
replies
2.0k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater
SingleCellExperiment
BiocParallel
scuttle
scran
3.1 years ago
enricoferrero
▴ 660
4
votes
5
replies
2.9k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran
SingleCellExperiment
scuttle
scater
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
enricoferrero
▴ 660
5
votes
4
replies
7.0k
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: Running multiple KNN queries in parallel
by
SamGG
▴ 360
Thank you for your detailed answer, I appreciate it and your work.
Answer: Running multiple KNN queries in parallel
by
Aaron Lun
★ 28k
That is correct - you can't pass the prebuilt objects to different processes. Maybe `MulticoreParam()` might work on POSIX systems but I'm …
Answer: RSubread output significantly different from bash Subread output
by
Gordon Smyth
52k
The difference (as ATpoint has correctly pointed out) is that Rsubread::featureCounts counts multi-mapping reads by default whereas the com…
Answer: Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
by
Michael Love
43k
I would check the rank of your model matrix, and perhaps meet with a local statistician who can help you create an appropriate design matri…
Comment: sva: get a sv for RIN scores
by
gabriel.hoffman
▴ 170
Agreed. I'll add that with small sample size, a covariate can explain some fraction of expression variation even under the null.
Votes
Answer: Running multiple KNN queries in parallel
Answer: Running multiple KNN queries in parallel
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Answer: How to annotate a limma Elist raw class object with an annotation file
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