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StageR
•
reset
0
votes
10
replies
1.2k
views
Two treatments, one control
DESeq2
stageR
4 months ago
alephreish
• 0
0
votes
2
replies
596
views
Swimming downstream: transcript fold changes
DEXSeq
stageR
13 months ago
jbono
▴ 10
0
votes
1
reply
726
views
stageR p-adj values of zero
stageR
updated 3.1 years ago by
Koen Van den Berge
▴ 180 • written 3.2 years ago by
giwa.ao
• 0
0
votes
1
reply
998
views
stageR with input from DRIMSeq
DRIMSeq
stageR
updated 5.7 years ago by
Koen Van den Berge
▴ 180 • written 5.7 years ago by
sdvie
• 0
2
votes
4
replies
1.9k
views
stageR: Error in stageWiseAdjustment
stageR
rnaseqDTU
DRIMSeq
DEXSeq
5.8 years ago
d-joester
▴ 20
4
votes
4
replies
1.5k
views
Correct use of Nested/Stage-wise testing with limma/stageR for 3-group design.
limma
stageR
decideTests
updated 5.9 years ago by
Koen Van den Berge
▴ 180 • written 5.9 years ago by
maltethodberg
▴ 180
0
votes
3
replies
1.3k
views
Post-hoc filtering on the standard deviation in proportions
drimseq
rnaseqdtu
stager
updated 6.0 years ago by
Michael Love
43k • written 6.0 years ago by
Jack.Hearn
• 0
1
vote
5
replies
1.8k
views
Plotting Expression of Differential Transcripts plotDEXseq
DEXSeq
StageR
rnaseqDTU
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
rbenel
▴ 40
2
votes
9
replies
2.1k
views
stageR NA in getAdjustedPValues() (method=dtu)
drimseq
stageR
dtu
salmon rna seq
updated 6.4 years ago by
Koen Van den Berge
▴ 180 • written 6.4 years ago by
fiona.dick91
▴ 60
9 results • Page
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Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
by
Aaron Lun
★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
Comment: contrast matrix design for a continuous variable
by
dtzhu337
• 0
Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable
by
Gordon Smyth
52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
Comment: fail to use addPerROIQC in Rmd
by
liu.n
• 0
That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd
by
joseph.joonsang
• 0
> dim(spe) [1] 19962 425
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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