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design
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2.0k
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DESeq2 comparison of treatment within tissue type, ignoring other tissue type
deseq2
comparison
design
paired
treatment
updated 5.8 years ago by
swbarnes2
★ 1.4k • written 5.8 years ago by
tinglec
• 0
0
votes
4
replies
2.4k
views
DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2
contrast
design
6.0 years ago
luciest.rodriguez
• 0
0
votes
2
replies
1.1k
views
different designs for finding DEG by limma
limma
DEG
design
6.1 years ago
amin.ghareyazi
• 0
0
votes
8
replies
2.8k
views
Two controls in RNAseq formula for DESeq2
deseq2
formula
controls
design
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
taveluz
• 0
0
votes
3
replies
1.4k
views
Analysis strategy - possible to use naive control group as t=0 for two treatment groups?
Deseq2
design
time course
basal group
updated 6.2 years ago by
Michael Love
43k • written 6.2 years ago by
Rob Buurstede
• 0
4
votes
18
replies
27k
views
DEseq2 time-series design.
deseq2
timecourse
design
updated 6.2 years ago by
simon baldwin
• 0 • written 10.9 years ago by
shao
▴ 100
0
votes
1
reply
871
views
DESeq2 analysis of multifactorial RNAseq experiment
deseq2
design
time-course
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
Victor Chano
• 0
1
vote
1
reply
1.3k
views
All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2
differential expression
batch correction
design
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
wunderl
▴ 40
0
votes
1
reply
1.2k
views
Perform time course rna seq analysis at once with a single design or separate differential analysis for each time point
deseq2
design
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
adhikb
• 0
3
votes
3
replies
1.1k
views
Extracting within subject effect in a between and within subject model with DESeq2
deseq2
design
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
i.sudbery
▴ 40
3
votes
5
replies
1.9k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 6.5 years ago by
Aaron Lun
★ 29k • written 6.5 years ago by
Pietro
▴ 40
3
votes
4
replies
1.8k
views
Paired analysis (tumor vs normal) at three different conditions with EdgeR
edger
design
matrix
de
updated 6.6 years ago by
Aaron Lun
★ 29k • written 6.6 years ago by
takumima
▴ 10
0
votes
7
replies
2.0k
views
Problems with DESeq2 'design' parameter using Shiny/rhandsontable
deseq2
shiny
design
rhandsontable
hot_to_r()
updated 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
hinkel2
• 0
0
votes
1
reply
812
views
DESeq2 3 factor design - whether to split up data or add interaction terms
deseq2
design
updated 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
atongz652
• 0
0
votes
2
replies
2.1k
views
DESeq2- multifactor design- 3 conditions and 3 timepoints
deseq2
design
updated 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
bioinfo
• 0
3
votes
6
replies
3.8k
views
Limma design/contrast correct?
limma
microarray
design
paired
mixed model
updated 6.6 years ago by
Aaron Lun
★ 29k • written 6.6 years ago by
rasmus.agren
• 0
4
votes
7
replies
4.2k
views
LIMMA time series spline model.matrix design setup
limma
design
model.matrix
time series
splines
updated 6.6 years ago by
Aaron Lun
★ 29k • written 6.6 years ago by
tleona3
• 0
1
vote
2
replies
1.2k
views
DESeq2 design with different cell lines and disease status
deseq2
design
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
lu.ne
• 0
0
votes
7
replies
1.7k
views
DeSeq2 Ribosome Profiling: multiple factor design
deseq2
design
timeseries
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
indrik.wijaya
▴ 20
7
votes
7
replies
9.7k
views
DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
deseq2
LRT
rnaseq
design
reduced model
updated 6.8 years ago by
evocanres
• 0 • written 8.4 years ago by
I.Castanho
▴ 50
5
votes
6
replies
2.1k
views
How to set up appropriate analysis using sample type and condition for DESeq2
deseq2
differential gene expression
design
updated 6.9 years ago by
Michael Love
43k • written 6.9 years ago by
newbio17
• 0
0
votes
5
replies
1.8k
views
DESeq2 design formula - correlation with ordered variable
DESeq2
design
formula
matrix
updated 7.3 years ago by
Michael Love
43k • written 7.3 years ago by
t.kuilman
▴ 170
2
votes
4
replies
1.3k
views
Limma model for paired and pool together
limma
design
rnaseq
updated 7.4 years ago by
Ryan C. Thompson
★ 7.9k • written 7.4 years ago by
b.nota
▴ 370
0
votes
6
replies
2.2k
views
DESeq2 It is correct to use interaction term for patient variability?
deseq2
design
interaction term
R
written 7.6 years ago by
briverog
• 0
1
vote
8
replies
2.0k
views
design versus interaction term similarities and/or differences?
deseq2
ANOVA
design
interaction term
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
tarun2
• 0
1
vote
2
replies
2.1k
views
DESeq2 - Design for TCGA unpaired RNAseq data
DESeq2
design
TCGA
unpaired
RNAseq
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
Talip
▴ 10
0
votes
5
replies
2.3k
views
Limma: how to account for twin data (both MZ and DZ twins)?
limma
design
RNA-seq
formula
twins
updated 7.9 years ago by
Aaron Lun
★ 29k • written 7.9 years ago by
Simone
• 0
3
votes
7
replies
2.5k
views
DESeq2 design formula: how to account for twin data (MZ and DZ)?
DESeq2
twins
design
formula
RNA-seq
7.9 years ago
Simone
• 0
2
votes
4
replies
1.6k
views
design microarrays limma
limma
statistical power
design
variability
microarray
updated 8.0 years ago by
Aaron Lun
★ 29k • written 8.0 years ago by
roser.navarro
• 0
0
votes
1
reply
1.9k
views
intra-sample time series comparison using DESeq2
deseq2
time course
rnaseq
design
contrast
updated 8.5 years ago by
Michael Love
43k • written 8.5 years ago by
prppmet
• 0
4
votes
13
replies
3.4k
views
Which formula should I use to set the best model matrix for my analysis ?
DESEQ2
EDGER
design
8.9 years ago
ZheFrench
▴ 60
3
votes
4
replies
2.7k
views
Deseq2 DE between WT and MUTANT normalised with respect to control
deseq2
multiple factor design
design and contrast matrix
design
multifactorial design
9.0 years ago
shimbalama
• 0
4
votes
3
replies
8.0k
views
deseq2 warning for the design formula
deseq2
design
updated 9.6 years ago by
Michael Love
43k • written 9.6 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
1.2k
views
Need assistance with complicated DESeq2 design
DESeq2
design
9.8 years ago
alex.pelletier
▴ 10
2
votes
3
replies
1.7k
views
how to set design for 2-dye Agilent array experiment with common reference group?
limma
2-dye
agilent
common reference
design
updated 9.8 years ago by
James W. MacDonald
68k • written 9.8 years ago by
Guido Hooiveld
★ 4.1k
1
vote
1
reply
1.1k
views
Best formula to use for this experimental setup
deseq2
differential gene expression
design
updated 10.2 years ago by
Michael Love
43k • written 10.3 years ago by
bdg
• 0
0
votes
0
replies
1.8k
views
Job:
Come apply for our Epidemiologist, AncestryHealth role
genomics
genetics
design
statistics
scientist
Job
10.3 years ago
careers
• 0
3
votes
13
replies
3.0k
views
Design and independent filtering of patient RNA-seq data
differential gene expression
deseq2
design
independent filtering
limma
updated 10.3 years ago by
James W. MacDonald
68k • written 10.3 years ago by
mat.lesche
▴ 110
2
votes
3
replies
3.3k
views
Help with DESeq2 Multiple Factor Design
deseq2
design
multiple factor design
updated 10.5 years ago by
Bernd Klaus
▴ 610 • written 10.5 years ago by
asaferali
• 0
2
votes
8
replies
3.0k
views
DESeq design question
deseq2
design
10.9 years ago • updated 10.5 years ago
sunkid
• 0
1
vote
1
reply
6.1k
views
Not full rank design using Deseq2
deseq2
design
counts
updated 10.6 years ago by
Michael Love
43k • written 10.6 years ago by
Rainy Gorilla
▴ 30
0
votes
3
replies
3.7k
views
Where to include an interaction term in DESeq2
deseq2
contrast
design
updated 10.7 years ago by
Michael Love
43k • written 10.7 years ago by
ksilkaitis
• 0
6
votes
6
replies
3.3k
views
design matrix for 4 groups in edgeR
edger
design
10.9 years ago
alakatos
▴ 130
93 results • Page
2 of 2
Recent ...
Replies
Comment: Sharing a collection of datasets in ExperimentHub
by
Peter Hickey
▴ 760
The [**scRNAseq**](https://bioconductor.org/packages/scRNAseq/) package ([source on GitHub](https://github.com/LTLA/scRNAseq)) might serve …
Answer: EuroBioC2023 abstract submission is open!
by
efuite222
• 0
Abstract submissions are now open for the #EuroBioC2023 conference in Ghent, Belgium, from September 20-22; submit by April 14 for opportu…
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
by
ReinholdGaylord99
• 0
Thank you so much! https://www.nature.com/articles/s41467-021-25960-2/ [geometry dash lite](https://geometrydashlite.online)
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
Gordon Smyth
53k
I'm not sure that I understand. You have a dataset that, even after pseudo-bulking, still has 6000 samples? That is surprising. Retaining …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
abaed
• 0
Hello again @gordonsmyth, I've now applied the analysis using a more detailed annotation of cell types/clusters, which includes about 100 …
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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