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10x
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0
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Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
7 months ago
rocanja
▴ 60
0
votes
1
reply
917
views
Choosing the right lower limit for emptyDrops
SingleCell
emptyDrops
10X
updated 18 months ago by
Peter Hickey
▴ 740 • written 18 months ago by
sandra.garces.19
• 0
0
votes
2
replies
883
views
Compare and filter three BAM files
RNAseq
10X
19 months ago
wt215
• 0
4
votes
5
replies
3.1k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
2.3 years ago • updated 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
2.9k
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
7.8k
views
How to identify real cells in 10X RNA-seq ?
single-cell
10X
Cell calling
DropletUtils
cellranger
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
xingxd16
▴ 20
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Comment: Combining RNAseq and microarray data using edgeR/limma-voom
by
Adam Marstrand
• 0
Thank you!
Comment: Combining RNAseq and microarray data using edgeR/limma-voom
by
Adam Marstrand
• 0
Hi Gordon, Thanks for the answer! This makes a lot of sense. Your suggested pipeline (separate processing of datasets -> gene set analyses…
Comment: How many of my genes from my gene list are in each KEGG pathway?
by
josephasmith1310
• 0
> You can compare the number in the column setSize versus the number of > genes in core_enrichment. The former corresponds to the number of…
Comment: EuroBioC2024 abstract submission is open!
by
Esperan
• 0
Great information about the EuroBioC2024 conference! https://openreview.net/group?id=bioconductor.org/EuroBioC/2024/Conferences [slope](htt…
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
by
Gordon Smyth
51k
I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…
Votes
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
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