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paired
•
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0
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0
replies
741
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Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount
csaw
paired
2.5 years ago
julie.chevalier
• 0
1
vote
6
replies
1.8k
views
DESeq2 design for paired samples
DESeq2
paired
updated 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
annamariabugaj
▴ 10
0
votes
1
reply
1.5k
views
Subject paired DESeq2 design
DESeq2
paired
design
updated 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
dr
▴ 10
1
vote
15
replies
3.9k
views
between and within subjects design with batch correction
RNASeqData
BatchEffect
paired
DESeq2
4.7 years ago
demisa
• 0
0
votes
0
replies
930
views
PROPER for paired samples
PROPER
Paired
5.4 years ago
christoph8
• 0
2
votes
6
replies
2.1k
views
Nested design matrix in edgeR
edger
limma
paired
blocking
ruvseq
updated 5.6 years ago by
Gordon Smyth
53k • written 5.7 years ago by
ScA
• 0
1
vote
1
reply
953
views
DESeq2 paired test (for most samples)
deseq2
paired
tumor vs normal
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
dagsbio
• 0
1
vote
2
replies
1.3k
views
Correct DESeq2 interaction design and results with paired and nested data
deseq2
Paired
Nested
updated 6.0 years ago by
Michael Love
43k • written 6.0 years ago by
julia.chariker
▴ 10
0
votes
1
reply
2.0k
views
DESeq2 comparison of treatment within tissue type, ignoring other tissue type
deseq2
comparison
design
paired
treatment
updated 6.1 years ago by
swbarnes2
★ 1.4k • written 6.1 years ago by
tinglec
• 0
1
vote
3
replies
1.6k
views
How can I run a paired RankProd analysis in R?
RankProd
paired
RNAseq
R
updated 6.2 years ago by
James W. MacDonald
68k • written 6.2 years ago by
joker33
• 0
1
vote
2
replies
2.6k
views
Pair-wise Limma Analysis with time series data and two levels (control and treatment)
limma
microarray
time series
DEG
paired
updated 6.3 years ago by
Gordon Smyth
53k • written 6.3 years ago by
kawess
• 0
6
votes
6
replies
2.3k
views
Limma DEG analysis experiment with partial paired design + batch effect
limma
paired
batch
updated 6.3 years ago by
Gordon Smyth
53k • written 6.3 years ago by
english.server
▴ 20
3
votes
3
replies
1.3k
views
Paired design in limma
limma
paired
updated 6.9 years ago by
Aaron Lun
★ 29k • written 6.9 years ago by
rasmus.agren
• 0
0
votes
1
reply
965
views
Paired samples in DESeq2
R
deseq2
Paired
Samples
updated 6.9 years ago by
Michael Love
43k • written 6.9 years ago by
m.wekking
• 0
3
votes
6
replies
3.9k
views
Limma design/contrast correct?
limma
microarray
design
paired
mixed model
updated 6.9 years ago by
Aaron Lun
★ 29k • written 6.9 years ago by
rasmus.agren
• 0
4
votes
9
replies
2.4k
views
limma paired design with continous covariate
limma
paired
covariate
updated 9.6 years ago by
Steve Lianoglou
★ 13k • written 9.6 years ago by
meeta.mistry
▴ 30
3
votes
3
replies
2.4k
views
read counts of paired end reads for DESeq2 analysis
deseq
featurecounts
paired
updated 9.7 years ago by
Steve Lianoglou
★ 13k • written 9.7 years ago by
tszn1984
• 0
1
vote
5
replies
2.3k
views
diffHic preparePairs() does not identify paired-end reads
diffHic
preparePairs
paired
BAM
updated 9.9 years ago by
Aaron Lun
★ 29k • written 9.9 years ago by
ilyco
• 0
1
vote
9
replies
4.5k
views
LIMMA for paired analysis with adjustment for confounding continuous variables
limma
gene expression
confounding
adjustment
paired
10.2 years ago
Loodramon
• 0
0
votes
2
replies
1.7k
views
Using merged alignments of PE readlists for DEXSeq
dexseq
paired
rnaseq
samtools merge
updated 10.4 years ago by
Alejandro Reyes
★ 1.9k • written 10.4 years ago by
arom2
• 0
0
votes
1
reply
1.6k
views
WGCNA package with monozygotic twin data
wgcna
Twin Analysis
within-pair analysis
paired
updated 10.6 years ago by
Peter Langfelder
★ 3.0k • written 10.6 years ago by
mahes.muniandy
• 0
4
votes
7
replies
3.9k
views
Correct implementation of multifactorial paired analysis in limma software package for DE expression
limma
microarray
multiple factor design
paired
updated 10.9 years ago by
Gordon Smyth
53k • written 10.9 years ago by
svlachavas
▴ 840
2
votes
1
reply
2.0k
views
EdgeR: Accounting for batch effects in a pairwise analysis
paired
batcheffect
updated 10.9 years ago by
Gordon Smyth
53k • written 10.9 years ago by
cinderelliedoll
• 0
4
votes
14
replies
6.5k
views
Including technical and biological replicates in Limma block analysis?
limma
microarray
block
paired
linear model
11.1 years ago
vas
▴ 40
7
votes
15
replies
17k
views
DESeq2 paired multifactor test
deseq2
paired
updated 3.1 years ago by
teabonng
• 0 • written 11.2 years ago by
hwillenbrock
▴ 20
1
vote
6
replies
4.1k
views
Limma: advice needed for best approach for joint paired and unpaired analyses in unbalanced intervention study
limma
paired
unpaired
duplicateCorrelation
updated 11.2 years ago by
bcbio_uk
▴ 10 • written 11.2 years ago by
Guido Hooiveld
★ 4.1k
1
vote
5
replies
2.5k
views
limma paired design matrix 3 factors
limma
paired
design and contrast matrix
11.2 years ago
wim.trypsteen
• 0
27 results • Page
1 of 1
Recent ...
Replies
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Dear Johannes, Would it be possible to generate a EnsDb for the newest Medicago V5 genome release? Medicago truncatula A17 r5.0 This woul…
Answer: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond
by
Ludwig Geistlinger
▴ 80
When referring to the OSCA book including individual sub-books please cite the OSCA paper: Amezquita, R.A., Lun, A.T.L., Becht, E. et a…
Votes
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
how to control age and gender effect in expression data using DESeq2
Answer: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond
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