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simpleSingleCell
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4
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5
replies
2.0k
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emptyDrops identified less non-empty cells with lower total UMI counts?
DropletUtils
scRNA-seq
emptyDrops
simplesinglecell
cell calling
updated 3.5 years ago by
Aaron Lun
★ 28k • written 4.7 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 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
Angelos Armen
• 0
1
vote
1
reply
675
views
Feature selection across batches in simpleSingleCell "Correcting batch effects" vignette
simpleSingleCell
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
Angelos Armen
• 0
5
votes
1
reply
4.5k
views
Error with DropletUtils::EmptyDrops()
DropletUtils
EmptyDrops
simpleSingleCell
updated 21 months ago by
Stefano Mangiola
▴ 10 • written 4.8 years ago by
shbrief
▴ 20
1
vote
5
replies
1.6k
views
Preprocessing in scran::doubletCells
scran
simpleSingleCell
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
Angelos Armen
• 0
4
votes
4
replies
2.8k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma
edgeR
simplesingleCell
scran
scater
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
Bogdan
▴ 670
4
votes
2
replies
1.6k
views
single cell data: adding random effects for subject with multilevel experiment design
SingleCellExperiment
scran
limma
simpleSingleCell
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
Matt Mulé
• 0
1
vote
3
replies
1.7k
views
Troubles with barcodeRanks()
DropletUtils
SingleCellExperiement
DelayedArray
simpleSingleCell
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
Steve Pederson
▴ 170
7
votes
2
replies
2.4k
views
Recommendations for combining multiple 10x runs into one SingleCellExperiment
singlecellexperiment
dropletutils
simplesinglecell
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
Peter Hickey
▴ 740
0
votes
1
reply
855
views
Unusual graph for Identifying HVGs from the normalized log-expression
workflows
simplesinglecell
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
es.azadian
• 0
0
votes
1
reply
950
views
The explanation of plotExplanatoryVariables plot
simplesinglecell
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
Xingyu
• 0
1
vote
2
replies
1.8k
views
SingleCellExperiment object cannot be used by Scater package?
scater
singlecellexperiment
simplesinglecell
updated 6.2 years ago by
Aaron Lun
★ 28k • written 6.2 years ago by
Xingyu
• 0
3
votes
2
replies
3.1k
views
Sparse matrices in Bioconductor objects for single-cell analyses
scater
simpleSingleCell
workflows
updated 6.9 years ago by
Aaron Lun
★ 28k • written 6.9 years ago by
sandmann.t
▴ 70
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I looked into the genomic distributions. Please see the screenshot attatched ![ distrubution for female loci, boot1 and boot2][1] how do …
Answer: How to save the DEXSeq results
by
Michael Love
41k
If you look at the output here: https://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html#4_Testing_for_differe…
Answer: Method to find pathways different between 2 groups
by
Robert Castelo
★ 3.3k
Hi, regarding how could you combine the result from each tool, one option is using a so-called "ensembl method", for instance, the package …
Answer: Couldn't connect to server while using "pathways"
by
James W. MacDonald
65k
As ATpoint already noted, you should proceed from the assumption that your audience knows nothing about what you are doing, and provide eno…
Answer: Trim/Filter out-of-bounds GRanges
by
Michael Love
41k
https://support.bioconductor.org/p/73432/#73448
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Answer: Method to find pathways different between 2 groups
Answer: Method to find pathways different between 2 groups
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
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