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10X
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4
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`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
20 months ago
Peter Hickey
▴ 710
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
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
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
▴ 710
0
votes
2
replies
601
views
Compare and filter three BAM files
RNAseq
10X
13 months ago
wt215
• 0
0
votes
1
reply
644
views
Choosing the right lower limit for emptyDrops
SingleCell
emptyDrops
10X
updated 11 months ago by
Peter Hickey
▴ 710 • written 11 months ago by
sandra.garces.19
• 0
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
0
votes
2
replies
182
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
29 days ago
rocanja
▴ 60
8 results • Page
1 of 1
Recent ...
Replies
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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