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sc3
•
reset
0
votes
3
replies
3.9k
views
Installing SC3: gfortran error on Mac M1
SC3
4.3 years ago
krp
• 0
1
vote
4
replies
2.4k
views
number of cell clusters in scRNA-seq
scran
scater
sc3
updated 6.6 years ago by
Aaron Lun
★ 29k • written 6.6 years ago by
Bogdan
▴ 670
0
votes
7
replies
3.3k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater
limma
scde
scran
sc3
6.6 years ago
Bogdan
▴ 670
4
votes
5
replies
2.6k
views
Using SC3 with batch corrected MNN values
SC3
Scater
Scran
scRNA-Seq
Batch Correction
updated 6.8 years ago by
Vladimir Kiselev
▴ 150 • written 6.8 years ago by
hamza_karakurt
▴ 60
0
votes
2
replies
1.4k
views
error running sc3_plot_de_genes in SC3 R package
SC3
updated 6.9 years ago by
Vladimir Kiselev
▴ 150 • written 6.9 years ago by
weiqiao1029
• 0
0
votes
1
reply
1.8k
views
SC3 how to customize plots ?
SC3
plot
consensus
marker
heatmap
updated 7.1 years ago by
Vladimir Kiselev
▴ 150 • written 7.1 years ago by
shaktirielland
• 0
0
votes
2
replies
1.3k
views
Failure to cluster SC3
SC3
updated 7.3 years ago by
Vladimir Kiselev
▴ 150 • written 7.3 years ago by
jhopkins
• 0
1
vote
1
reply
2.0k
views
A question about log_transformed
SC3
updated 7.5 years ago by
James W. MacDonald
68k • written 7.5 years ago by
liushang
• 0
0
votes
2
replies
1.4k
views
How can I show certain gene's expression in clusters by sc3
sc3
updated 7.7 years ago by
Vladimir Kiselev
▴ 150 • written 7.7 years ago by
qq1493438060
• 0
1
vote
1
reply
1.3k
views
Is there a way to pull out the stability index matrix from the SC3 object?
sc3
updated 7.9 years ago by
Vladimir Kiselev
▴ 150 • written 8.0 years ago by
yingzi.zhang
▴ 10
0
votes
1
reply
1.7k
views
SC3 Package: marker genes and normal genes obtained from featureData
SC3
updated 8.0 years ago by
Vladimir Kiselev
▴ 150 • written 8.1 years ago by
angela.ubn
• 0
1
vote
1
reply
2.1k
views
Batch effect removal before SC3?
SC3
batch effect
removebatcheffect
updated 8.1 years ago by
Vladimir Kiselev
▴ 150 • written 8.1 years ago by
muad.abdelhay
▴ 10
1
vote
8
replies
3.2k
views
SC3_estimate_k formatting error?
sc3
scater
updated 8.1 years ago by
Vladimir Kiselev
▴ 150 • written 8.2 years ago by
alexandriapinto1
▴ 10
5
votes
2
replies
7.7k
views
Raw count data for SC3 and SingleCellExperiment set problem
singlecellexperiment
sc3
scater
updated 8.2 years ago by
Vladimir Kiselev
▴ 150 • written 8.2 years ago by
chengyuzou
▴ 10
4
votes
5
replies
2.7k
views
SC3 gene clusters
SC3
single cell
single-cell
Tutorial
updated 8.2 years ago by
Martin Morgan
25k • written 8.2 years ago by
ahmed.elewa
▴ 20
1
vote
1
reply
2.0k
views
Does SC3 correct counts for gene length?
sc3
scater
single-cell
rna-seq
biclustering
updated 8.4 years ago by
Vladimir Kiselev
▴ 150 • written 8.4 years ago by
firestar
▴ 20
0
votes
1
reply
4.1k
views
Import .mtx file in R
sc3
updated 8.6 years ago by
Vladimir Kiselev
▴ 150 • written 8.6 years ago by
suman70532
• 0
4
votes
2
replies
1.9k
views
sc3_plot_expression, colour labels
sc3
single-cell
updated 8.6 years ago by
Vladimir Kiselev
▴ 150 • written 8.6 years ago by
cfustero
▴ 20
3
votes
3
replies
1.9k
views
Sharing SC3_interactive results
SC3
single-cell
shiny
updated 8.7 years ago by
Vladimir Kiselev
▴ 150 • written 8.7 years ago by
cfustero
▴ 20
4
votes
3
replies
2.5k
views
using SC3 and scater for bulk-RNAseq
sc3
scater
scRNAseq
updated 8.9 years ago by
Vladimir Kiselev
▴ 150 • written 8.9 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
5
replies
2.5k
views
sc3_prepare function error
sc3
scater
single-cell
single cell
updated 8.9 years ago by
Vladimir Kiselev
▴ 150 • written 8.9 years ago by
Assa Yeroslaviz
★ 1.5k
3
votes
2
replies
1.7k
views
SC3 tutorial error
SC3
updated 9.2 years ago by
Vladimir Kiselev
▴ 150 • written 9.2 years ago by
Jenn
▴ 30
3
votes
1
reply
1.8k
views
SC3 with latent variable corrected counts
SC3
single cell
updated 9.2 years ago by
Vladimir Kiselev
▴ 150 • written 9.2 years ago by
Mark
▴ 10
23 results • Page
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ja569116
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Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
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It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
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The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
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I updated the above answer today.
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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…
Votes
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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