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DESeq2
•
reset
9
votes
12
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 16 hours ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
5
votes
12
replies
2.1k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 days ago by
Seyram M.
• 0 • written 4.6 years ago by
hsbio
▴ 10
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 18 days ago by
Wolfgang Huber
★ 13k • written 9 months ago by
Jane
▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 1 day ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
3
replies
635
views
DESeq2 setting significant p-value
DESeq2
updated 18 hours ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
0
votes
4
replies
553
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 2 days ago by
Michael Love
41k • written 5 months ago by
Crystal571
• 0
0
votes
7
replies
396
views
DESeq2 filtering vs edgeR filtering
DESeq2
5 weeks ago • updated 23 days ago
fr8712ca-s
• 0
1
vote
6
replies
391
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 15 days ago by
Michael Love
41k • written 15 days ago by
RL
• 0
2
votes
3
replies
310
views
PCA of different bacterial species
DESeq2
updated 22 days ago by
Michael Love
41k • written 23 days ago by
Laura
▴ 10
0
votes
2
replies
273
views
DESeq filtering specific to contrasts
DESeq2
updated 21 hours ago by
Carlin95
• 0 • written 9 weeks ago by
Emma
• 0
2
votes
3
replies
270
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 29 days ago by
Michael Love
41k • written 4 weeks ago by
andrebolerbarros
▴ 20
0
votes
3
replies
228
views
Help with Complex DESeq2 Design
DESeq2
updated 29 days ago by
ATpoint
★ 4.0k • written 4 weeks ago by
kelsey.beavers
• 0
0
votes
4
replies
214
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 16 days ago by
Michael Love
41k • written 17 days ago by
Aidan
• 0
0
votes
2
replies
213
views
Regressing out batch effects
DESeq2
updated 9 days ago by
Michael Love
41k • written 14 days ago by
kys91240
• 0
0
votes
2
replies
195
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
29 days ago • updated 28 days ago
kcarey
• 0
1
vote
2
replies
195
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
28 days ago • updated 22 days ago
Chanderkant Chaudhary
• 0
3
votes
2
replies
188
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
24 days ago
Anita
▴ 10
0
votes
2
replies
178
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 9 days ago by
Michael Love
41k • written 13 days ago by
nhaus
▴ 30
0
votes
3
replies
172
views
DEG with low counts
DESeq2
4 days ago • updated 2 days ago
Rajat
• 0
1
vote
1
reply
160
views
How to retrieve detailed regression results from deseq2
DESeq2
updated 3 days ago by
Michael Love
41k • written 8 days ago by
Weiqian
▴ 10
1
vote
2
replies
151
views
Design Matrix within group comparison more than two groups
DESeq2
6 days ago • updated 5 days ago
hemantcnaik
• 0
0
votes
1
reply
146
views
collapseReplicates dimension error
DESeq2
Dese
updated 24 days ago by
Michael Love
41k • written 27 days ago by
Léa
• 0
1
vote
1
reply
144
views
DESeq2 - Missing values in count matrix
DESeq2
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
Hong Thu
• 0
0
votes
1
reply
141
views
DESeq2 gives an error and R crashes
DESeq2
8 days ago • updated 7 days ago
Shefali
• 0
0
votes
2
replies
140
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
16 days ago • updated 15 days ago
michelafrancesconi8
• 0
0
votes
3
replies
138
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 2 days ago by
Michael Love
41k • written 3 days ago by
andrebolerbarros
▴ 20
0
votes
1
reply
131
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 21 days ago by
Michael Love
41k • written 21 days ago by
Mikushi
• 0
0
votes
2
replies
130
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
joshua.mannheimer
• 0
1
vote
1
reply
127
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
16 days ago • updated 15 days ago
Layal
• 0
0
votes
1
reply
126
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 9 days ago by
Michael Love
41k • written 9 days ago by
Adelaide
• 0
0
votes
1
reply
107
views
Bioinformatics student
Des
DESeq2
updated 6 days ago by
hemantcnaik
• 0 • written 6 days ago by
Sahar
• 0
0
votes
1
reply
94
views
Deseq2 Rlog transformation
DESeq2
updated 3 days ago by
ATpoint
★ 4.0k • written 5 days ago by
Sahar
• 0
0
votes
1
reply
70
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 19 hours ago by
ATpoint
★ 4.0k • written 1 day ago by
quanah.hudson
• 0
0
votes
1
reply
69
views
covariate with negative and positive values
DESeq2
updated 15 hours ago by
Michael Love
41k • written 2 days ago by
Brynn
• 0
0
votes
2
replies
61
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
1 day ago • updated 1 hour ago
lonn
• 0
0
votes
1
reply
50
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 15 hours ago by
Michael Love
41k • written 1 day ago by
ussarizona
• 0
0
votes
1
reply
41
views
rlog transformation
DESeq2
updated 15 hours ago by
Michael Love
41k • written 21 hours ago by
ishij9717
• 0
0
votes
1
reply
38
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 15 hours ago by
Michael Love
41k • written 21 hours ago by
09191919
• 0
38 results • Page
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Replies
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
Thank you for your suggestions! Here is the MA plot: ![enter image description here][1] I tried several normalization methods with DiffBi…
Answer: OrgDb for maize
by
Guido Hooiveld
★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question
by
Garrett
• 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
alserg
▴ 240
They are reorder in the decreasing order.
Votes
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
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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