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Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
5 weeks ago
rocanja
▴ 60
0
votes
1
reply
657
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
0
votes
2
replies
620
views
Compare and filter three BAM files
RNAseq
10X
13 months ago
wt215
• 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
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
5
votes
3
replies
1.3k
views
Latent factors for differential expression
deseq2
zinbwave
10X
scRNA-seq
Differential expression
updated 3.8 years ago by
Michael Love
41k • written 3.8 years ago by
vincent.croset
▴ 20
4
votes
2
replies
2.3k
views
When to combine samples in the pre-processing of 10x scRNA-seq data?
10x
scrna-seq
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
jma1991
▴ 70
7
votes
12
replies
7.0k
views
How to identify real cells in 10X RNA-seq ?
single-cell
10X
Cell calling
DropletUtils
cellranger
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
xingxd16
▴ 20
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1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
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For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
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Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
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Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
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