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simpleSingleCell
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reset
4
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5
replies
2.5k
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emptyDrops identified less non-empty cells with lower total UMI counts?
DropletUtils
scRNA-seq
emptyDrops
simplesinglecell
cell calling
updated 4.5 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
C T
▴ 140
4
votes
6
replies
1.6k
views
Feature selection across batches in simpleSingleCell when spike-ins are not available.
simpleSingleCell
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
Angelos Armen
• 0
1
vote
1
reply
893
views
Feature selection across batches in simpleSingleCell "Correcting batch effects" vignette
simpleSingleCell
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
Angelos Armen
• 0
5
votes
1
reply
5.2k
views
Error with DropletUtils::EmptyDrops()
DropletUtils
EmptyDrops
simpleSingleCell
updated 2.7 years ago by
Stefano Mangiola
▴ 40 • written 5.7 years ago by
shbrief
▴ 20
1
vote
5
replies
2.1k
views
Preprocessing in scran::doubletCells
scran
simpleSingleCell
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
Angelos Armen
• 0
4
votes
4
replies
3.3k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma
edgeR
simplesingleCell
scran
scater
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
Bogdan
▴ 670
4
votes
2
replies
2.1k
views
single cell data: adding random effects for subject with multilevel experiment design
SingleCellExperiment
scran
limma
simpleSingleCell
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
Matt Mulé
• 0
1
vote
3
replies
2.0k
views
Troubles with barcodeRanks()
DropletUtils
SingleCellExperiement
DelayedArray
simpleSingleCell
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
Steve Pederson
▴ 170
8
votes
2
replies
3.3k
views
Recommendations for combining multiple 10x runs into one SingleCellExperiment
singlecellexperiment
dropletutils
simplesinglecell
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
Peter Hickey
▴ 750
0
votes
1
reply
1.1k
views
Unusual graph for Identifying HVGs from the normalized log-expression
workflows
simplesinglecell
updated 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
es.azadian
• 0
0
votes
1
reply
1.1k
views
The explanation of plotExplanatoryVariables plot
simplesinglecell
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
Xingyu
• 0
1
vote
2
replies
2.1k
views
SingleCellExperiment object cannot be used by Scater package?
scater
singlecellexperiment
simplesinglecell
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
Xingyu
• 0
3
votes
2
replies
3.9k
views
Sparse matrices in Bioconductor objects for single-cell analyses
scater
simpleSingleCell
workflows
updated 7.8 years ago by
Aaron Lun
★ 28k • written 7.8 years ago by
sandmann.t
▴ 70
13 results • Page
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Answer: Model performance for spline modelling of RNA-seq timecourses in edgeR
by
Gordon Smyth
52k
I don't understand your question, because there is no difference between limma or glmFit or glmQLFit in terms of spline modeling or the tes…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
by
Luca
• 0
Perhaps edgeR's upperquartile normalization handles this better, the MA looks a lot more centered at 0 ![enter image description here][1]…
Answer: DESeq2 - am I extracting results incorrectly?
by
James W. MacDonald
68k
If I assume that Followup gets converted to T3 and Treatment to LowSug somewhere along the line (and therefore GroupTreatment.Followup is G…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
by
Luca
• 0
I noticed the dual populations as well, when using csaw this is controlled for. Regarding the DE profile, given this disease condition we e…
Answer: Origin of the labels for the SingleCellMultiModal dataset
by
ATpoint
★ 4.8k
If you check the underlying code a bit you find that there is a file with data sources: ```r modes_file <- system.file("extdata", "metadat…
Votes
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder
Comment: DESeq - help with pair wise comparisons
Answer: Is random access by row index possible for an indexed VCF file?
Answer: Is random access by row index possible for an indexed VCF file?
Answer: SingleR with multiple single cell references
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