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Deseq2
•
reset
9
votes
12
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 1 day ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
5
votes
14
replies
2.1k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 18 hours ago by
Seyram M.
• 0 • written 4.6 years ago by
hsbio
▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 2 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
5
replies
669
views
DESeq2 setting significant p-value
DESeq2
updated 19 hours ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
1
vote
2
replies
195
views
How to retrieve detailed regression results from deseq2
DESeq2
9 days ago • updated 15 hours ago
Weiqian
▴ 10
1
vote
2
replies
156
views
Design Matrix within group comparison more than two groups
DESeq2
7 days ago • updated 6 days ago
hemantcnaik
• 0
0
votes
1
reply
62
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
ussarizona
• 0
0
votes
1
reply
54
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 1 day ago by
Michael Love
41k • written 2 days ago by
09191919
• 0
0
votes
1
reply
57
views
rlog transformation
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
ishij9717
• 0
0
votes
4
replies
201
views
DEG with low counts
DESeq2
updated 22 hours ago by
Michael Love
41k • written 5 days ago by
Rajat
• 0
0
votes
7
replies
355
views
DESeq filtering specific to contrasts
DESeq2
updated 18 hours ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
0
votes
4
replies
132
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
2 days ago • updated 3 hours ago
lonn
• 0
0
votes
1
reply
104
views
Deseq2 Rlog transformation
DESeq2
updated 4 days ago by
ATpoint
★ 4.0k • written 6 days ago by
Sahar
• 0
0
votes
3
replies
149
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 3 days ago by
Michael Love
41k • written 4 days ago by
andrebolerbarros
▴ 20
0
votes
4
replies
556
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 3 days ago by
Michael Love
41k • written 5 months ago by
Crystal571
• 0
0
votes
1
reply
82
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 1 day ago by
ATpoint
★ 4.0k • written 2 days ago by
quanah.hudson
• 0
0
votes
1
reply
80
views
covariate with negative and positive values
DESeq2
updated 1 day ago by
Michael Love
41k • written 3 days ago by
Brynn
• 0
17 results • Page
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Replies
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Robert Castelo
★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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Robert Castelo
★ 3.2k
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James W. MacDonald
65k
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shepherl
3.8k
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BioinfGuru
▴ 30
Popular Question
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Gordon Smyth
50k
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