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simplesinglecell
•
reset
4
votes
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
674
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 4.7 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 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
Peter Hickey
▴ 740
0
votes
1
reply
853
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
949
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: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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