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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 19 hours ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
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
2
votes
5
replies
693
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
0
votes
4
replies
227
views
DEG with low counts
DESeq2
updated 4 days ago by
Michael Love
41k • written 9 days ago by
Rajat
• 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
0
votes
4
replies
188
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
6 days ago • updated 4 days ago
lonn
• 0
3
votes
3
replies
138
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 19 hours ago by
Michael Love
41k • written 1 day ago by
WardDeb
• 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
107
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
1
reply
93
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
1
vote
1
reply
87
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 7 hours ago by
Michael Love
41k • written 15 hours ago by
i.sudbery
▴ 40
0
votes
1
reply
84
views
rlog transformation
DESeq2
updated 5 days ago by
Michael Love
41k • written 5 days ago by
ishij9717
• 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
3
replies
62
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 1 hour ago by
ATpoint
★ 4.0k • written 17 hours ago by
Aaliya
• 0
0
votes
2
replies
11
views
Different Shrunk Log2FC according with reference
DESeq2
1 hour ago • updated 52 minutes ago
andrebolerbarros
▴ 20
0
votes
0
replies
10
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
1 hour ago
winwater0928
• 0
18 results • Page
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Replies
Comment: Trying to use enrichGO
by
Guido Hooiveld
★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference
by
andrebolerbarros
▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
ATpoint
★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference
by
ATpoint
★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
Gayatri
• 0
What I meant is even after deleting the NCBI.sqlite file, and re-running the script, an empty NCBI.sqlite file (0 kb) is created which is c…
Votes
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
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ATpoint
★ 4.0k
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Gordon Smyth
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i.sudbery
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Michael Love
41k
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shepherl
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