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10X
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Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
11 months ago
rocanja
▴ 60
0
votes
1
reply
1.1k
views
Choosing the right lower limit for emptyDrops
SingleCell
emptyDrops
10X
updated 21 months ago by
Peter Hickey
▴ 750 • written 21 months ago by
sandra.garces.19
• 0
0
votes
2
replies
961
views
Compare and filter three BAM files
RNAseq
10X
23 months ago
wt215
• 0
4
votes
5
replies
3.4k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
2.5 years ago
Peter Hickey
▴ 750
1
vote
1
reply
1.3k
views
Number of non-empty drops returned by emptyDrops() depends on value of test.ambience
DropletUtils
emptyDrops
10x
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
Peter Hickey
▴ 750
5
votes
3
replies
1.7k
views
Latent factors for differential expression
deseq2
zinbwave
10X
scRNA-seq
Differential expression
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
vincent.croset
▴ 20
4
votes
2
replies
3.1k
views
When to combine samples in the pre-processing of 10x scRNA-seq data?
10x
scrna-seq
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
jma1991
▴ 70
7
votes
12
replies
8.2k
views
How to identify real cells in 10X RNA-seq ?
single-cell
10X
Cell calling
DropletUtils
cellranger
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
xingxd16
▴ 20
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Answer: To count or not to count multi-overlapping reads?
by
Gordon Smyth
52k
> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…
Comment: Weird p-values using DESeq2?
by
ATpoint
★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2?
by
Wolfgang Huber
★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
Comment: How to visualize these pathways using pathview
by
ingrid.h
• 0
Yes I have seen it, thanks.
Comment: Store Matrix in DataFrame Cell
by
Dario Strbenac
★ 1.6k
It does not appear to work. > DataFrame(name = "test", value = list(matrix(1:4, ncol = 2))) DataFrame with 2 rows and 3 columns …
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