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stageR
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0
votes
10
replies
1.7k
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Two treatments, one control
DESeq2
stageR
10 months ago • updated 9 months ago
alephreish
• 0
0
votes
2
replies
715
views
Swimming downstream: transcript fold changes
DEXSeq
stageR
18 months ago
jbono
▴ 10
0
votes
1
reply
824
views
stageR p-adj values of zero
stageR
updated 3.6 years ago by
Koen Van den Berge
▴ 180 • written 3.6 years ago by
giwa.ao
• 0
0
votes
1
reply
1.1k
views
stageR with input from DRIMSeq
DRIMSeq
stageR
updated 6.2 years ago by
Koen Van den Berge
▴ 180 • written 6.2 years ago by
sdvie
• 0
2
votes
4
replies
2.0k
views
stageR: Error in stageWiseAdjustment
stageR
rnaseqDTU
DRIMSeq
DEXSeq
6.3 years ago
d-joester
▴ 20
4
votes
4
replies
1.7k
views
Correct use of Nested/Stage-wise testing with limma/stageR for 3-group design.
limma
stageR
decideTests
updated 6.3 years ago by
Koen Van den Berge
▴ 180 • written 6.3 years ago by
maltethodberg
▴ 180
0
votes
3
replies
1.4k
views
Post-hoc filtering on the standard deviation in proportions
drimseq
rnaseqdtu
stager
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
Jack.Hearn
• 0
1
vote
5
replies
2.0k
views
Plotting Expression of Differential Transcripts plotDEXseq
DEXSeq
StageR
rnaseqDTU
updated 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
rbenel
▴ 50
2
votes
9
replies
2.3k
views
stageR NA in getAdjustedPValues() (method=dtu)
drimseq
stageR
dtu
salmon rna seq
updated 6.8 years ago by
Koen Van den Berge
▴ 180 • written 6.8 years ago by
fiona.dick91
▴ 60
9 results • Page
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Comment: European Bioconductor Conference 2023 planning
by
rasafreelancer
• 0
@[chill guy clicker][1] Sounds like a fantastic opportunity! I'm really curious about the emerging technologies that will be highlighted at…
Answer: How to extract coordinates of mismatches from a BAM file lodaded in as a GAlignm
by
Hervé Pagès
16k
This should be fast: ```r library(GenomicAlignments) extractMismatchesFromGAlignments <- function(ga) { stopifnot(is(ga, "GAlign…
Answer: GAlignments Cigar to GRanges
by
Hervé Pagès
16k
```r > as(gal, "GRangesList") GRangesList object of length 2: [[1]] GRanges object with 2 ranges and 0 metadata columns: seqnames …
Comment: DESEq2 comparison with mulitple cell types under 2 conditions
by
boczniak767
▴ 740
Dear @mikelove , this method is very appealing but does it avoid making not meaningful comparisons like "1KO" vs "2WT" (using example fro…
Comment: AnnotationHub/ExperimentHub resources backup
by
James W. MacDonald
68k
You can always grab things from the cache if you want to save or share, but that's not part of the paradigm, so there aren't direct facilit…
Votes
When running contrasts, does it use normalized read counts?
When running contrasts, does it use normalized read counts?
Importing Salmon counts with tximport with host and virus genomes
Normalization / size factors of samples with high expression of few genes (viral infection)
A: Mult-way interaction design in limma
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