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Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment
SingleCell
SingleCellWorkflow
SingleCellData
4 months ago
Ludwig Geistlinger
▴ 80
1
vote
3
replies
1.3k
views
Possible issue following the logNormCounts(filtered) with resulted fit
single-cell
SingleCell
SingleCellExperiment
SingleCellWorkflow
SingleCellData
8 months ago • updated 7 months ago
Konstantinos Yeles
▴ 90
2
votes
4
replies
2.2k
views
How to detect LacZ tagged cells from single cell
SingleCell
SingleCellExperiment
SingleCellWorkflow
SingleCellData
updated 5 months ago by
Partly
• 0 • written 3.4 years ago by
k1m
▴ 20
2
votes
4
replies
1.7k
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Summary of library size factor is all equal to one
SingleCell
SingleCellData
SingleCellWorkflow
SingleCellExperiment
3.4 years ago
Romina
• 0
0
votes
0
replies
1.2k
views
Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow
DifferentialExpression
SingleCell
SingleCellMultiModal
MAST
3.6 years ago
Nik Tuzov
▴ 90
2
votes
2
replies
4.2k
views
After having the output from SingleR for cell type annotation, what's the next step to assign the cell type to each cluster
SingleCellSignalR
SingleCellWorkflow
SingleR
updated 2.2 years ago by
Assa Yeroslaviz
★ 1.5k • written 4.7 years ago by
FantasticAI
▴ 10
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ja569116
• 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice
by
Gordon Smyth
53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
I updated the above answer today.
Answer: When to use edgeR or limma
by
James W. MacDonald
68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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Thomas Girke
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