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sc3
•
reset
0
votes
3
replies
3.3k
views
Installing SC3: gfortran error on Mac M1
SC3
3.5 years ago
krp
• 0
1
vote
4
replies
2.0k
views
number of cell clusters in scRNA-seq
scran
scater
sc3
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
Bogdan
▴ 670
0
votes
7
replies
2.8k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater
limma
scde
scran
sc3
5.8 years ago
Bogdan
▴ 670
4
votes
5
replies
2.3k
views
Using SC3 with batch corrected MNN values
SC3
Scater
Scran
scRNA-Seq
Batch Correction
updated 6.0 years ago by
Vladimir Kiselev
▴ 150 • written 6.0 years ago by
hamza_karakurt
▴ 60
0
votes
2
replies
1.2k
views
error running sc3_plot_de_genes in SC3 R package
SC3
updated 6.1 years ago by
Vladimir Kiselev
▴ 150 • written 6.1 years ago by
weiqiao1029
• 0
0
votes
1
reply
1.6k
views
SC3 how to customize plots ?
SC3
plot
consensus
marker
heatmap
updated 6.3 years ago by
Vladimir Kiselev
▴ 150 • written 6.3 years ago by
shaktirielland
• 0
0
votes
2
replies
1.1k
views
Failure to cluster SC3
SC3
updated 6.5 years ago by
Vladimir Kiselev
▴ 150 • written 6.5 years ago by
jhopkins
• 0
1
vote
1
reply
1.7k
views
A question about log_transformed
SC3
updated 6.7 years ago by
James W. MacDonald
68k • written 6.7 years ago by
liushang
• 0
0
votes
2
replies
1.2k
views
How can I show certain gene's expression in clusters by sc3
sc3
updated 6.8 years ago by
Vladimir Kiselev
▴ 150 • written 6.8 years ago by
qq1493438060
• 0
1
vote
1
reply
1.1k
views
Is there a way to pull out the stability index matrix from the SC3 object?
sc3
updated 7.1 years ago by
Vladimir Kiselev
▴ 150 • written 7.1 years ago by
yingzi.zhang
▴ 10
0
votes
1
reply
1.5k
views
SC3 Package: marker genes and normal genes obtained from featureData
SC3
updated 7.2 years ago by
Vladimir Kiselev
▴ 150 • written 7.3 years ago by
angela.ubn
• 0
1
vote
1
reply
1.9k
views
Batch effect removal before SC3?
SC3
batch effect
removebatcheffect
updated 7.3 years ago by
Vladimir Kiselev
▴ 150 • written 7.3 years ago by
muad.abdelhay
▴ 10
1
vote
8
replies
2.9k
views
SC3_estimate_k formatting error?
sc3
scater
updated 7.3 years ago by
Vladimir Kiselev
▴ 150 • written 7.4 years ago by
alexandriapinto1
▴ 10
5
votes
2
replies
7.0k
views
Raw count data for SC3 and SingleCellExperiment set problem
singlecellexperiment
sc3
scater
updated 7.4 years ago by
Vladimir Kiselev
▴ 150 • written 7.4 years ago by
chengyuzou
▴ 10
4
votes
5
replies
2.3k
views
SC3 gene clusters
SC3
single cell
single-cell
Tutorial
updated 7.4 years ago by
Martin Morgan
25k • written 7.4 years ago by
ahmed.elewa
▴ 20
1
vote
1
reply
1.7k
views
Does SC3 correct counts for gene length?
sc3
scater
single-cell
rna-seq
biclustering
updated 7.5 years ago by
Vladimir Kiselev
▴ 150 • written 7.6 years ago by
firestar
▴ 20
0
votes
1
reply
3.8k
views
Import .mtx file in R
sc3
updated 7.8 years ago by
Vladimir Kiselev
▴ 150 • written 7.8 years ago by
suman70532
• 0
4
votes
2
replies
1.7k
views
sc3_plot_expression, colour labels
sc3
single-cell
updated 7.8 years ago by
Vladimir Kiselev
▴ 150 • written 7.8 years ago by
cfustero
▴ 20
3
votes
3
replies
1.6k
views
Sharing SC3_interactive results
SC3
single-cell
shiny
updated 7.9 years ago by
Vladimir Kiselev
▴ 150 • written 7.9 years ago by
cfustero
▴ 20
4
votes
3
replies
2.2k
views
using SC3 and scater for bulk-RNAseq
sc3
scater
scRNAseq
updated 8.0 years ago by
Vladimir Kiselev
▴ 150 • written 8.0 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
5
replies
2.2k
views
sc3_prepare function error
sc3
scater
single-cell
single cell
updated 8.1 years ago by
Vladimir Kiselev
▴ 150 • written 8.1 years ago by
Assa Yeroslaviz
★ 1.5k
3
votes
2
replies
1.6k
views
SC3 tutorial error
SC3
updated 8.3 years ago by
Vladimir Kiselev
▴ 150 • written 8.3 years ago by
Jenn
▴ 30
3
votes
1
reply
1.6k
views
SC3 with latent variable corrected counts
SC3
single cell
updated 8.4 years ago by
Vladimir Kiselev
▴ 150 • written 8.4 years ago by
Mark
▴ 10
23 results • Page
1 of 1
Recent ...
Replies
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
by
James W. MacDonald
68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore
by
Kent
• 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore
by
Michael Love
43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi
by
Michael Love
43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Comment: deseq2 lfc shrinkage with few DEGs
by
Michael Love
43k
Agree with your edit.
Votes
A: use tximport's countsFromAbundance when using DESeq2
Comment: Using TPM from tximport of Salmon output for singscore
Answer: Using TPM from tximport of Salmon output for singscore
Comment: deseq2 lfc shrinkage with few DEGs
Answer: DESEQ2 looking at main effects while controlling for a continuous variable
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