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Deseq2
•
reset
0
votes
7
replies
402
views
DESeq2 filtering vs edgeR filtering
DESeq2
5 weeks ago • updated 24 days ago
fr8712ca-s
• 0
0
votes
4
replies
204
views
DEG with low counts
DESeq2
updated 1 day ago by
Michael Love
41k • written 5 days ago by
Rajat
• 0
5
votes
14
replies
2.2k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 23 hours ago by
Seyram M.
• 0 • written 4.6 years ago by
hsbio
▴ 10
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
1
vote
2
replies
202
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
29 days ago • updated 23 days ago
Chanderkant Chaudhary
• 0
1
vote
2
replies
199
views
How to retrieve detailed regression results from deseq2
DESeq2
9 days ago • updated 19 hours ago
Weiqian
▴ 10
0
votes
1
reply
84
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 2 days ago by
ATpoint
★ 4.0k • written 3 days ago by
quanah.hudson
• 0
0
votes
2
replies
203
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
4 weeks ago • updated 29 days ago
kcarey
• 0
2
votes
5
replies
672
views
DESeq2 setting significant p-value
DESeq2
updated 23 hours ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
0
votes
7
replies
358
views
DESeq filtering specific to contrasts
DESeq2
updated 22 hours ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
0
votes
1
reply
82
views
covariate with negative and positive values
DESeq2
updated 1 day ago by
Michael Love
41k • written 3 days ago by
Brynn
• 0
0
votes
2
replies
185
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 10 days ago by
Michael Love
41k • written 15 days ago by
nhaus
▴ 30
1
vote
1
reply
131
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
18 days ago • updated 17 days ago
Layal
• 0
1
vote
6
replies
394
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 16 days ago by
Michael Love
41k • written 16 days ago by
RL
• 0
0
votes
1
reply
64
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 1 day ago by
Michael Love
41k • written 3 days ago by
ussarizona
• 0
0
votes
1
reply
56
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
59
views
rlog transformation
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
ishij9717
• 0
0
votes
1
reply
150
views
collapseReplicates dimension error
DESeq2
Dese
updated 25 days ago by
Michael Love
41k • written 29 days ago by
Léa
• 0
1
vote
1
reply
149
views
DESeq2 - Missing values in count matrix
DESeq2
updated 15 days ago by
James W. MacDonald
65k • written 16 days ago by
Hong Thu
• 0
0
votes
2
replies
216
views
Regressing out batch effects
DESeq2
updated 10 days ago by
Michael Love
41k • written 15 days ago by
kys91240
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 3 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
3
votes
2
replies
191
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
26 days ago • updated 25 days ago
Anita
▴ 10
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 19 days ago by
Wolfgang Huber
★ 13k • written 9 months ago by
Jane
▴ 10
2
votes
3
replies
317
views
PCA of different bacterial species
DESeq2
updated 24 days ago by
Michael Love
41k • written 24 days ago by
Laura
▴ 10
0
votes
4
replies
558
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
2
replies
135
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 15 days ago by
James W. MacDonald
65k • written 15 days ago by
joshua.mannheimer
• 0
0
votes
1
reply
137
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 22 days ago by
Michael Love
41k • written 22 days ago by
Mikushi
• 0
0
votes
1
reply
112
views
Bioinformatics student
Des
DESeq2
updated 7 days ago by
hemantcnaik
• 0 • written 7 days ago by
Sahar
• 0
0
votes
3
replies
151
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
andrebolerbarros
▴ 20
1
vote
2
replies
158
views
Design Matrix within group comparison more than two groups
DESeq2
7 days ago
hemantcnaik
• 0
0
votes
1
reply
132
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 10 days ago by
Michael Love
41k • written 10 days ago by
Adelaide
• 0
0
votes
4
replies
220
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 17 days ago by
Michael Love
41k • written 18 days ago by
Aidan
• 0
0
votes
2
replies
145
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
18 days ago • updated 17 days ago
michelafrancesconi8
• 0
0
votes
4
replies
138
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
2 days ago • updated 8 hours ago
lonn
• 0
0
votes
1
reply
106
views
Deseq2 Rlog transformation
DESeq2
updated 5 days ago by
ATpoint
★ 4.0k • written 6 days ago by
Sahar
• 0
0
votes
1
reply
147
views
DESeq2 gives an error and R crashes
DESeq2
9 days ago • updated 8 days ago
Shefali
• 0
36 results • Page
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Thanks Robert!
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…
Votes
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
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
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shepherl
3.8k
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