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simplesingleCell
•
reset
4
votes
5
replies
2.8k
views
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 6.2 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
999
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 6.3 years ago by
Aaron Lun
★ 29k • written 6.3 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 6.3 years ago by
Aaron Lun
★ 29k • written 6.3 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
1.3k
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 7.7 years ago by
Aaron Lun
★ 29k • written 7.7 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 8.4 years ago by
Aaron Lun
★ 29k • written 8.4 years ago by
sandmann.t
▴ 70
13 results • Page
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Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts
by
Michael Love
43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts
by
empty_mt
• 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts
by
Michael Love
43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Votes
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
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