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scuttle
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scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
scuttle
8 hours ago
Adam
• 0
2
votes
1
reply
534
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
937
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
9 results • Page
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Comment: contrast matrix design for a continuous variable
by
dtzhu337
• 0
Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable
by
Gordon Smyth
52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
Comment: fail to use addPerROIQC in Rmd
by
liu.n
• 0
That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd
by
joseph.joonsang
• 0
> dim(spe) [1] 19962 425
Comment: fail to use addPerROIQC in Rmd
by
liu.n
• 0
Hi, what's the output from `dim(spe)`?
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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