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10X
•
reset
0
votes
2
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530
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Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
7 months ago
rocanja
▴ 60
0
votes
1
reply
907
views
Choosing the right lower limit for emptyDrops
SingleCell
emptyDrops
10X
updated 17 months ago by
Peter Hickey
▴ 740 • written 18 months ago by
sandra.garces.19
• 0
0
votes
2
replies
874
views
Compare and filter three BAM files
RNAseq
10X
19 months ago
wt215
• 0
4
votes
5
replies
3.0k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
2.2 years ago
Peter Hickey
▴ 740
1
vote
1
reply
1.2k
views
Number of non-empty drops returned by emptyDrops() depends on value of test.ambience
DropletUtils
emptyDrops
10x
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
Peter Hickey
▴ 740
5
votes
3
replies
1.6k
views
Latent factors for differential expression
deseq2
zinbwave
10X
scRNA-seq
Differential expression
updated 4.3 years ago by
Michael Love
42k • written 4.3 years ago by
vincent.croset
▴ 20
4
votes
2
replies
2.8k
views
When to combine samples in the pre-processing of 10x scRNA-seq data?
10x
scrna-seq
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
jma1991
▴ 70
7
votes
12
replies
7.7k
views
How to identify real cells in 10X RNA-seq ?
single-cell
10X
Cell calling
DropletUtils
cellranger
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
xingxd16
▴ 20
8 results • Page
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Replies
Answer: Deseq to output continous sequencing data
by
Michael Love
42k
This what VST is for? Have you see the `rnaseqGene` workflow?
Answer: Adjusted p-values become NA when sub-setting samples
by
Michael Love
42k
One thing to do is just turn off `independentFiltering` altogether. If you know what are reasonable filters that maintain power by discardi…
Comment: Adjusted p-values become NA when sub-setting samples
by
Michael Love
42k
Just saw this post, for some reason I didn't get it the first time.
Comment: RNA-seq: samples form different experiments, how to do DGEs?
by
Philippine
• 0
Thank you, indeed I called them lab but their name should be Batch 1, 2, 3, 4, 5 and 6. Thank you again for your help! :D
Comment: Adjusted p-values become NA when sub-setting samples
by
txema.heredia
• 0
I have been back to this after a break. I have run a series of pairwise comparisons using either all the samples together, or only a subset…
Votes
Answer: BiocParallel error when running DiffBind
Answer: Robust way of dealing with low number of samples for Differential Gene Expressio
Comment: DiffBind GreyListChIP error: Error: BiocParallel errors
Answer: Robust way of dealing with low number of samples for Differential Gene Expressio
Answer: Robust way of dealing with low number of samples for Differential Gene Expressio
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