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simplesinglecell
•
reset
4
votes
5
replies
2.1k
views
emptyDrops identified less non-empty cells with lower total UMI counts?
DropletUtils
scRNA-seq
emptyDrops
simplesinglecell
cell calling
updated 3.7 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
C T
▴ 140
4
votes
6
replies
1.2k
views
Feature selection across batches in simpleSingleCell when spike-ins are not available.
simpleSingleCell
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
Angelos Armen
• 0
1
vote
1
reply
699
views
Feature selection across batches in simpleSingleCell "Correcting batch effects" vignette
simpleSingleCell
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
Angelos Armen
• 0
5
votes
1
reply
4.6k
views
Error with DropletUtils::EmptyDrops()
DropletUtils
EmptyDrops
simpleSingleCell
updated 23 months ago by
Stefano Mangiola
▴ 10 • written 4.9 years ago by
shbrief
▴ 20
1
vote
5
replies
1.7k
views
Preprocessing in scran::doubletCells
scran
simpleSingleCell
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
Angelos Armen
• 0
4
votes
4
replies
2.9k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma
edgeR
simplesingleCell
scran
scater
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
Bogdan
▴ 670
4
votes
2
replies
1.7k
views
single cell data: adding random effects for subject with multilevel experiment design
SingleCellExperiment
scran
limma
simpleSingleCell
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
Matt Mulé
• 0
1
vote
3
replies
1.7k
views
Troubles with barcodeRanks()
DropletUtils
SingleCellExperiement
DelayedArray
simpleSingleCell
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
Steve Pederson
▴ 170
7
votes
2
replies
2.5k
views
Recommendations for combining multiple 10x runs into one SingleCellExperiment
singlecellexperiment
dropletutils
simplesinglecell
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
Peter Hickey
▴ 740
0
votes
1
reply
888
views
Unusual graph for Identifying HVGs from the normalized log-expression
workflows
simplesinglecell
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
es.azadian
• 0
0
votes
1
reply
977
views
The explanation of plotExplanatoryVariables plot
simplesinglecell
updated 6.3 years ago by
Aaron Lun
★ 28k • written 6.3 years ago by
Xingyu
• 0
1
vote
2
replies
1.8k
views
SingleCellExperiment object cannot be used by Scater package?
scater
singlecellexperiment
simplesinglecell
updated 6.4 years ago by
Aaron Lun
★ 28k • written 6.4 years ago by
Xingyu
• 0
3
votes
2
replies
3.2k
views
Sparse matrices in Bioconductor objects for single-cell analyses
scater
simpleSingleCell
workflows
updated 7.0 years ago by
Aaron Lun
★ 28k • written 7.0 years ago by
sandmann.t
▴ 70
13 results • Page
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Comment: Ranking the GSEA Results
by
Lluís Revilla Sancho
▴ 730
You can have the ranking without the cutoff. If you don't keep any gene set after the cutoff then there is nothing to rank as you said, so…
Answer: Create a Graph w/ Only the Genes Interaction
by
Antonio
• 0
Thank you all, I solved my issue by creating a for loop. Cheers!
Comment: Ranking the GSEA Results
by
alserg
▴ 270
Apparently, it sends a notification to the developer on a new message after the tags were updated :) but not the change of tags itself
Comment: Ranking the GSEA Results
by
alserg
▴ 270
Where did you see ranking of genes by `log2FC * (-log10 p-value)`? I don't think I ever saw one and not sure what it should achieve. Aren't…
Comment: Trouble Installing DADA2 (warning: R new user)
by
shepherl
3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
Votes
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
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