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scuttle
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reset
2
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scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
scuttle
updated 8 months ago by
Aaron Lun
★ 29k • written 8 months ago by
Adam
▴ 10
2
votes
1
reply
877
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 17 months ago by
ATpoint
★ 4.9k • written 17 months ago by
Dario Strbenac
★ 1.6k
0
votes
3
replies
1.9k
views
Is logNormCounts log2 normalised counts as default?
scuttle
scater
updated 24 months ago by
ATpoint
★ 4.9k • written 24 months ago by
Abbi Edwards
• 0
1
vote
0
replies
2.6k
views
Convert SpatialExperiment Object to Seurat Object
scuttle
scater
seurat
SpatialExperiment
2.6 years ago
cathalgking
▴ 10
0
votes
1
reply
1.3k
views
cell_count column in SpatialExperiment Object
scuttle
scater
SpatialExperiment
updated 2.6 years ago by
alan.ocallaghan
▴ 160 • written 2.6 years ago by
cathalgking
▴ 10
2
votes
2
replies
2.0k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts
scran
librarySizeFactors
scuttle
scRNAseq
3.5 years ago
behr201
• 0
3
votes
3
replies
2.4k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater
SingleCellExperiment
BiocParallel
scuttle
scran
3.8 years ago
enricoferrero
▴ 680
4
votes
5
replies
3.6k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran
SingleCellExperiment
scuttle
scater
updated 4.6 years ago by
Aaron Lun
★ 29k • written 4.6 years ago by
enricoferrero
▴ 680
5
votes
4
replies
8.4k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran
scater
scuttle
updated 5.1 years ago by
Aaron Lun
★ 29k • written 5.1 years ago by
enricoferrero
▴ 680
9 results • Page
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Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
James W. MacDonald
68k
Your approach 1 is a bad idea. Subtracting the gene counts won't do what you want to do. I would personally check to see if there is any…
Comment: Can NanoString data be analyzed using DESeq2?
by
James W. MacDonald
68k
You can always discard, although you can also retain them to check for unexpected differences.
Comment: DESeq2 on NanoString Data
by
Michael Love
43k
Yes, if I discern a batch from EDA including looking at PCs, sample correlations, etc. It is close to SVA, we discuss both in the workflow…
Comment: DESeq2 on NanoString Data
by
thkapell
▴ 10
Thanks Michael. To this end, do you routinely use RUV or only when you detect a batch? It looks like it works in a similar fashion to SVA w…
Comment: Can NanoString data be analyzed using DESeq2?
by
thkapell
▴ 10
Thank you. I agree with your thoughts about the similarities of NanoString with RNA-seq. NanoString though, also has positive, negative pro…
Votes
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
Comment: Are voomByGroup and voomLmFit compatible?
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