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DESeq2
•
reset
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 5 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
6
votes
16
replies
2.2k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 11 hours ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
0
votes
4
replies
226
views
DEG with low counts
DESeq2
updated 4 days ago by
Michael Love
41k • written 9 days ago by
Rajat
• 0
0
votes
1
reply
91
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 5 days ago by
Michael Love
41k • written 6 days ago by
ussarizona
• 0
0
votes
1
reply
83
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 5 days ago by
Michael Love
41k • written 5 days ago by
09191919
• 0
0
votes
1
reply
83
views
rlog transformation
DESeq2
updated 5 days ago by
Michael Love
41k • written 5 days ago by
ishij9717
• 0
2
votes
5
replies
692
views
DESeq2 setting significant p-value
DESeq2
updated 4 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
0
votes
7
replies
383
views
DESeq filtering specific to contrasts
DESeq2
updated 4 days ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
1
vote
2
replies
215
views
How to retrieve detailed regression results from deseq2
DESeq2
13 days ago • updated 4 days ago
Weiqian
▴ 10
3
votes
3
replies
132
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 12 hours ago by
Michael Love
41k • written 1 day ago by
WardDeb
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 6 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
0
votes
1
reply
109
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 5 days ago by
ATpoint
★ 4.0k • written 6 days ago by
quanah.hudson
• 0
0
votes
1
reply
105
views
covariate with negative and positive values
DESeq2
updated 5 days ago by
Michael Love
41k • written 7 days ago by
Brynn
• 0
0
votes
4
replies
184
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
6 days ago • updated 3 days ago
lonn
• 0
1
vote
0
replies
31
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
7 hours ago
i.sudbery
▴ 40
0
votes
1
reply
38
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 3 hours ago by
swbarnes2
★ 1.3k • written 10 hours ago by
Aaliya
• 0
16 results • Page
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Recent ...
Replies
Answer: Citation for edgeR user guide
by
Gordon Smyth
50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class?
by
James W. MacDonald
65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp
by
clacarion
• 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Comment: minfi::read.metharray.exp
by
clacarion
• 0
Thank you for your response Basti ! I add all the idat files in a unique folder called "idat" and add it in my path ```r > list.files("…
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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i.sudbery
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Michael Love
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