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emptyDrops
•
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0
votes
2
replies
195
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
5 weeks ago
rocanja
▴ 60
0
votes
1
reply
653
views
Choosing the right lower limit for emptyDrops
SingleCell
emptyDrops
10X
updated 11 months ago by
Peter Hickey
▴ 740 • written 11 months ago by
sandra.garces.19
• 0
4
votes
5
replies
2.3k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
21 months ago • updated 20 months ago
Peter Hickey
▴ 740
5
votes
1
reply
4.4k
views
Error with DropletUtils::EmptyDrops()
DropletUtils
EmptyDrops
simpleSingleCell
updated 20 months ago by
Stefano Mangiola
▴ 10 • written 4.7 years ago by
shbrief
▴ 20
1
vote
1
reply
1.0k
views
Number of non-empty drops returned by emptyDrops() depends on value of test.ambience
DropletUtils
emptyDrops
10x
updated 3.3 years ago by
Aaron Lun
★ 28k • written 3.3 years ago by
Peter Hickey
▴ 740
4
votes
5
replies
2.0k
views
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
0
votes
2
replies
1.0k
views
Scalability of emptyDrops() running times
dropletutils
emptydrops
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
rosano
• 0
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Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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