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10X
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7
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12
replies
7.0k
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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
4
votes
5
replies
2.2k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
20 months ago
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
0
votes
2
replies
192
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
4 weeks ago
rocanja
▴ 60
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
0
votes
2
replies
607
views
Compare and filter three BAM files
RNAseq
10X
13 months ago
wt215
• 0
0
votes
1
reply
648
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
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 3.2 years ago by
Aaron Lun
★ 28k • written 3.2 years ago by
Peter Hickey
▴ 740
8 results • Page
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Answer: Why p value inconsistent when using different number of pathway score?
by
ATpoint
★ 4.0k
Same answer as here: https://support.bioconductor.org/p/9157606/ Adding or removing data (samples, genes, pathways, observations...) chang…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Thanks Robert!
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Robert Castelo
★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Votes
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
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