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DEseq2
•
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0
votes
2
replies
24
views
Different Shrunk Log2FC according with reference
DESeq2
2 hours ago
andrebolerbarros
▴ 20
0
votes
3
replies
64
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 2 hours ago by
ATpoint
★ 4.0k • written 19 hours ago by
Aaliya
• 0
0
votes
0
replies
14
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
2 hours ago
winwater0928
• 0
1
vote
1
reply
94
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 8 hours ago by
Michael Love
41k • written 16 hours ago by
i.sudbery
▴ 40
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 20 hours ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
3
votes
3
replies
139
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 21 hours ago by
Michael Love
41k • written 1 day ago by
WardDeb
• 0
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
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
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
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
4
replies
227
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
84
views
rlog transformation
DESeq2
updated 5 days ago by
Michael Love
41k • written 6 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 6 days ago by
09191919
• 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
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
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
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
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
4
replies
563
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 7 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
3
replies
170
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 7 days ago by
Michael Love
41k • written 8 days ago by
andrebolerbarros
▴ 20
0
votes
1
reply
109
views
Deseq2 Rlog transformation
DESeq2
updated 8 days ago by
ATpoint
★ 4.0k • written 10 days ago by
Sahar
• 0
1
vote
2
replies
163
views
Design Matrix within group comparison more than two groups
DESeq2
11 days ago • updated 10 days ago
hemantcnaik
• 0
0
votes
1
reply
115
views
Bioinformatics student
Des
DESeq2
updated 11 days ago by
hemantcnaik
• 0 • written 11 days ago by
Sahar
• 0
0
votes
1
reply
153
views
DESeq2 gives an error and R crashes
DESeq2
13 days ago • updated 12 days ago
Shefali
• 0
0
votes
2
replies
191
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 14 days ago by
Michael Love
41k • written 18 days ago by
nhaus
▴ 30
0
votes
1
reply
135
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 14 days ago by
Michael Love
41k • written 14 days ago by
Adelaide
• 0
0
votes
2
replies
219
views
Regressing out batch effects
DESeq2
updated 14 days ago by
Michael Love
41k • written 19 days ago by
kys91240
• 0
0
votes
2
replies
142
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 18 days ago by
James W. MacDonald
65k • written 18 days ago by
joshua.mannheimer
• 0
1
vote
1
reply
152
views
DESeq2 - Missing values in count matrix
DESeq2
updated 19 days ago by
James W. MacDonald
65k • written 19 days ago by
Hong Thu
• 0
1
vote
6
replies
400
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 20 days ago by
Michael Love
41k • written 20 days ago by
RL
• 0
0
votes
2
replies
149
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
21 days ago
michelafrancesconi8
• 0
1
vote
1
reply
135
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
21 days ago
Layal
• 0
0
votes
4
replies
229
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 21 days ago by
Michael Love
41k • written 22 days ago by
Aidan
• 0
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 23 days ago by
Wolfgang Huber
★ 13k • written 9 months ago by
Jane
▴ 10
0
votes
1
reply
140
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 26 days ago by
Michael Love
41k • written 26 days ago by
Mikushi
• 0
1
vote
2
replies
211
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
4 weeks ago • updated 27 days ago
Chanderkant Chaudhary
• 0
2
votes
3
replies
320
views
PCA of different bacterial species
DESeq2
updated 27 days ago by
Michael Love
41k • written 28 days ago by
Laura
▴ 10
0
votes
7
replies
406
views
DESeq2 filtering vs edgeR filtering
DESeq2
5 weeks ago • updated 28 days ago
fr8712ca-s
• 0
0
votes
1
reply
157
views
collapseReplicates dimension error
DESeq2
Dese
updated 29 days ago by
Michael Love
41k • written 4 weeks ago by
Léa
• 0
3
votes
2
replies
196
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
29 days ago
Anita
▴ 10
0
votes
2
replies
210
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
4 weeks ago
kcarey
• 0
2
votes
3
replies
283
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 4 weeks ago by
Michael Love
41k • written 5 weeks ago by
andrebolerbarros
▴ 20
0
votes
3
replies
242
views
Help with Complex DESeq2 Design
DESeq2
updated 5 weeks ago by
ATpoint
★ 4.0k • written 5 weeks ago by
kelsey.beavers
• 0
4
votes
7
replies
676
views
DESeq2 unable to handle large count values
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 5 months ago by
robennet
• 0
1
vote
1
reply
163
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2
ctsGE
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Emma
• 0
0
votes
1
reply
132
views
Help with DESeqDataSetFromHTSeqCount
DESeq2
RSeqAn
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
rahaf.nazzal9
• 0
0
votes
1
reply
163
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Yuqin
• 0
2
votes
2
replies
206
views
With DESeq2 "Not full rank" Error with design
DESeq2
DEs
5 weeks ago
feather-W
• 0
1
vote
3
replies
367
views
DEseq2 coefficient
DESeq2
coefficient
8 weeks ago • updated 5 weeks ago
JKim
• 0
4
votes
4
replies
1.1k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2
Dese
DifferentialRegulation
differe
updated 5 weeks ago by
feather-W
• 0 • written 12 months ago by
Bernardo
▴ 10
50 results • Page
1 of 1
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Replies
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs
by
Guangchuang Yu
★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
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…
Votes
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
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