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7
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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
2
replies
2.2k
views
When to combine samples in the pre-processing of 10x scRNA-seq data?
10x
scrna-seq
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
jma1991
▴ 70
4
votes
5
replies
2.2k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
20 months ago • updated 19 months ago
Peter Hickey
▴ 670
5
votes
3
replies
1.3k
views
Latent factors for differential expression
deseq2
zinbwave
10X
scRNA-seq
Differential expression
updated 3.7 years ago by
Michael Love
41k • written 3.7 years ago by
vincent.croset
▴ 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 3.2 years ago by
Aaron Lun
★ 28k • written 3.2 years ago by
Peter Hickey
▴ 670
0
votes
1
reply
621
views
Choosing the right lower limit for emptyDrops
SingleCell
emptyDrops
10X
updated 10 months ago by
Peter Hickey
▴ 670 • written 10 months ago by
sandra.garces.19
• 0
0
votes
2
replies
583
views
Compare and filter three BAM files
RNAseq
10X
12 months ago
wt215
• 0
0
votes
2
replies
139
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
10 days ago • updated 9 days ago
rocanja
▴ 60
8 results • Page
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Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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