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simplesingleCell
•
reset
4
votes
5
replies
2.8k
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emptyDrops identified less non-empty cells with lower total UMI counts?
DropletUtils
scRNA-seq
emptyDrops
simplesinglecell
cell calling
updated 5.0 years ago by
Aaron Lun
★ 29k • written 6.1 years ago by
C T
▴ 140
4
votes
6
replies
1.8k
views
Feature selection across batches in simpleSingleCell when spike-ins are not available.
simpleSingleCell
updated 6.2 years ago by
Aaron Lun
★ 29k • written 6.2 years ago by
Angelos Armen
• 0
1
vote
1
reply
979
views
Feature selection across batches in simpleSingleCell "Correcting batch effects" vignette
simpleSingleCell
updated 6.2 years ago by
Aaron Lun
★ 29k • written 6.2 years ago by
Angelos Armen
• 0
5
votes
1
reply
5.5k
views
Error with DropletUtils::EmptyDrops()
DropletUtils
EmptyDrops
simpleSingleCell
updated 3.2 years ago by
Stefano Mangiola
▴ 40 • written 6.2 years ago by
shbrief
▴ 20
1
vote
5
replies
2.3k
views
Preprocessing in scran::doubletCells
scran
simpleSingleCell
updated 6.2 years ago by
Aaron Lun
★ 29k • written 6.2 years ago by
Angelos Armen
• 0
4
votes
4
replies
3.6k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma
edgeR
simplesingleCell
scran
scater
updated 6.2 years ago by
Aaron Lun
★ 29k • written 6.2 years ago by
Bogdan
▴ 670
4
votes
2
replies
2.3k
views
single cell data: adding random effects for subject with multilevel experiment design
SingleCellExperiment
scran
limma
simpleSingleCell
updated 6.4 years ago by
Aaron Lun
★ 29k • written 6.4 years ago by
Matt Mulé
• 0
1
vote
3
replies
2.2k
views
Troubles with barcodeRanks()
DropletUtils
SingleCellExperiement
DelayedArray
simpleSingleCell
updated 6.4 years ago by
Aaron Lun
★ 29k • written 6.4 years ago by
Steve Pederson
▴ 170
8
votes
2
replies
3.6k
views
Recommendations for combining multiple 10x runs into one SingleCellExperiment
singlecellexperiment
dropletutils
simplesinglecell
updated 7.0 years ago by
Aaron Lun
★ 29k • written 7.0 years ago by
Peter Hickey
▴ 760
0
votes
1
reply
1.2k
views
Unusual graph for Identifying HVGs from the normalized log-expression
workflows
simplesinglecell
updated 7.1 years ago by
Aaron Lun
★ 29k • written 7.1 years ago by
es.azadian
• 0
0
votes
1
reply
1.3k
views
The explanation of plotExplanatoryVariables plot
simplesinglecell
updated 7.6 years ago by
Aaron Lun
★ 29k • written 7.6 years ago by
Xingyu
• 0
1
vote
2
replies
2.3k
views
SingleCellExperiment object cannot be used by Scater package?
scater
singlecellexperiment
simplesinglecell
updated 7.6 years ago by
Aaron Lun
★ 29k • written 7.6 years ago by
Xingyu
• 0
3
votes
2
replies
4.1k
views
Sparse matrices in Bioconductor objects for single-cell analyses
scater
simpleSingleCell
workflows
updated 8.3 years ago by
Aaron Lun
★ 29k • written 8.3 years ago by
sandmann.t
▴ 70
13 results • Page
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Recent ...
Replies
Comment: Help with defining groups
by
Phinney, Brett
▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness
by
massimo
• 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package
by
ksankaran
• 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
by
ATpoint
★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes
by
ATpoint
★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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