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Showing :
Deseq2
•
reset
16
votes
40
replies
8.3k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 2.2 years ago by
Clara
• 0 • written 4.7 years ago by
lim6432
▴ 50
5
votes
27
replies
3.6k
views
DESeq2 model - How to test case/control time course model when taking account within sample variability?
deseq2
multiple time points
time course
casecontrol
model design
updated 3.3 years ago by
Michael Love
41k • written 6.7 years ago by
heikki.sarin
▴ 10
1
vote
26
replies
5.9k
views
How can I install DeSeq2 in Jupyter Notebook?
deseq2
updated 5.1 years ago by
Marc Saric
▴ 70 • written 5.1 years ago by
david.wheeler7
▴ 20
0
votes
25
replies
2.8k
views
deseq2 course experiment
deseq2
6.8 years ago
ribioinfo
▴ 100
18
votes
24
replies
14k
views
[DESeq2] time series strain-specific differences over time
deseq2
timecourse
updated 3.1 years ago by
ethicalhackers
• 0 • written 9.0 years ago by
john
▴ 120
2
votes
23
replies
3.4k
views
Coping with a label/class imbalance in DESeq2
deseq2
rnaseq
r
regression
updated 7.5 years ago by
Michael Love
41k • written 7.5 years ago by
bkellman
• 0
10
votes
23
replies
13k
views
Macbook M1 install genefilter failed
DESeq2
m1
macbook
genefilter
2.7 years ago • updated 16 months ago
soda
▴ 80
13
votes
22
replies
26k
views
DESEq2 Paired samples Before and after treatment
deseq2
paired samples
updated 5 weeks ago by
Michael Love
41k • written 7.8 years ago by
adesrichard
▴ 30
26
votes
22
replies
18k
views
DESeq2 for ChIP-seq differential peaks
deseq2
deseq
chipseq
updated 6.7 years ago by
k.vitting.seerup
▴ 120 • written 8.6 years ago by
tangming2005
▴ 190
1
vote
22
replies
4.7k
views
DESEq2 Large Memory When Parallel
deseq2
updated 6.4 years ago by
Michael Love
41k • written 6.4 years ago by
Jeff Granja
▴ 10
1
vote
22
replies
5.0k
views
DESeq2 for Ribosomal profiling analysis
deseq2
8.0 years ago
jxu006
▴ 10
4
votes
21
replies
11k
views
DESeq2 and ComBat
deseq2
combat
updated 8.2 years ago by
Bernd Klaus
▴ 610 • written 8.2 years ago by
ribioinfo
▴ 100
28
votes
21
replies
47k
views
deseq2 filter the low counts
deseq2
lowcount
updated 10 weeks ago by
Xiao
• 0 • written 9.1 years ago by
aristotele_m
▴ 40
33
votes
21
replies
14k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
9.5 years ago • updated 18 months ago
Michael Love
41k
0
votes
20
replies
2.3k
views
DESeq2 question: why I got discrepancy results for DEGs when using different ways setting up the models
DESeq2
DEGs
2.7 years ago
Ming
▴ 380
1
vote
20
replies
3.4k
views
Deseq2 installed, but there is no package called ‘Biostrings’
DESeq2
Install
updated 17 months ago by
James W. MacDonald
65k • written 17 months ago by
Hannah000111
• 0
2
votes
20
replies
2.6k
views
plotPCA in DESeq2
software error
deseq2
3.8 years ago
yueli7
▴ 20
0
votes
20
replies
2.1k
views
Different DESeq2 results (both FC and pvalue) by changing col/row orders in input
DESeq2
21 months ago
Weisheng
• 0
52
votes
20
replies
43k
views
Batch correction in DESeq2
rnaseq
batch effect
deseq2
combat
removebatcheffect()
updated 7.8 years ago by
adam
• 0 • written 8.3 years ago by
AB
▴ 110
3
votes
19
replies
5.6k
views
lfcShrink and factors with multiple levels
deseq2
lfcshrink
relevel
updated 6.4 years ago by
Michael Love
41k • written 6.4 years ago by
mat.lesche
▴ 90
14
votes
19
replies
8.8k
views
DESeq2 Model Design
DESeq2
linear model
model
updated 2.9 years ago by
Michael Love
41k • written 9.3 years ago by
andrew.j.skelton73
▴ 370
0
votes
19
replies
1.9k
views
Paired Difference Analysis
deseq2
R
differential gene expression
6.6 years ago • updated 6.5 years ago
nhua
• 0
14
votes
19
replies
19k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2
annotation
granges
updated 2.1 years ago by
Nadine
▴ 60 • written 9.4 years ago by
Darya Vanichkina
▴ 120
6
votes
19
replies
3.5k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2
timecourse
multiple factor design
RNAseq analysis
differential gene expression
updated 6.5 years ago by
Gavin Kelly
▴ 680 • written 6.5 years ago by
c.nicole
▴ 50
0
votes
18
replies
2.8k
views
DESeq2 in R_devel: a bug?
DESeq2
DESeq2
updated 10.1 years ago by
Michael Love
41k • written 10.1 years ago by
Sylvain Foisy
▴ 80
15
votes
18
replies
3.2k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2
edgeR
goana
GO
updated 2.0 years ago by
Gordon Smyth
50k • written 2.0 years ago by
Raito92
▴ 60
10
votes
18
replies
16k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2
batch effect
batch
4.8 years ago
Mozart
▴ 30
0
votes
18
replies
2.6k
views
Subset-ing Large DESeqDataSet for data extraction with contrast function
deseq2
updated 4.6 years ago by
Michael Love
41k • written 4.6 years ago by
l.s.wijaya
• 0
11
votes
18
replies
4.6k
views
What is the correct use of removeBatchEffect's design parameter
deseq2
limma
updated 3.0 years ago by
Gordon Smyth
50k • written 3.6 years ago by
Sam
▴ 10
5
votes
18
replies
2.7k
views
DESeq2 comparison two cell types and two genotypes
GeneExpressionWorkflow
DESeq2
GeneExpression
updated 2.9 years ago by
Michael Love
41k • written 2.9 years ago by
Yosapol
• 0
0
votes
18
replies
4.6k
views
DEseq2 metagenomic analysis without replicates
DESeq2
DESeq2
updated 10.2 years ago by
Kristina M Fontanez
▴ 220 • written 10.2 years ago by
Guest User
★ 13k
3
votes
18
replies
3.0k
views
DESeq2 filter out my expression gene
deseq2
updated 8.1 years ago by
Michael Love
41k • written 8.1 years ago by
jarod_v6@libero.it
▴ 40
8
votes
18
replies
12k
views
Batch correction by using ComBat function in sva package
deseq2
combat
Knownbatcheffect
Tutorial
updated 3.1 years ago by
Samuel Daniel
• 0 • written 4.5 years ago by
rajeshparmar4
▴ 10
1
vote
18
replies
4.0k
views
DESEQ2 linear model of dose
deseq2
updated 7.4 years ago by
Simon Anders
★ 3.7k • written 7.5 years ago by
jshouse
▴ 10
5
votes
18
replies
1.7k
views
Difference of difference, paired design
edger
deseq2
limma
updated 4.7 years ago by
swbarnes2
★ 1.3k • written 4.7 years ago by
Bloodgas
• 0
0
votes
18
replies
2.5k
views
DESeq2: Possible issue with colData and sorting
deseq2
summarizedexperiment
updated 7.5 years ago by
Martin Morgan
25k • written 7.5 years ago by
henrik.seidel
▴ 40
4
votes
18
replies
24k
views
DEseq2 time-series design.
deseq2
timecourse
design
updated 4.7 years ago by
simon baldwin
• 0 • written 9.4 years ago by
shao
▴ 100
4
votes
18
replies
5.8k
views
DESeq2 - multifactorial design
LRT
DESeq2
interaction
updated 3.0 years ago by
Kevin Blighe
★ 3.9k • written 3.1 years ago by
annamariabugaj
▴ 10
5
votes
18
replies
7.3k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor
Install
DESeq2
updated 3 months ago by
picasa1983
• 0 • written 2.2 years ago by
Victor
• 0
9
votes
17
replies
1.7k
views
DESeq2 design subcategories
deseq2
deseq
differential binding analysis
updated 6.3 years ago by
Michael Love
41k • written 6.3 years ago by
rbronste
▴ 60
7
votes
17
replies
5.3k
views
DESeqDataSetFromTximport: Error in checkSlotAssignment
deseq2
tximport
6.9 years ago
JWCarlson
▴ 80
2
votes
17
replies
1.6k
views
lfcshrink error DESeq2
DESeq2
lfcshrink
DESe
updated 10 months ago by
Michael Love
41k • written 10 months ago by
Alina
• 0
2
votes
17
replies
2.2k
views
Computationally Singular Matrices - DESeq
deseq2
rnaseq
sva
updated 17 months ago by
Michael Love
41k • written 5.0 years ago by
flippy23
• 0
0
votes
17
replies
7.6k
views
DESeq2 Error NA values
deseq2
updated 8.8 years ago by
Michael Love
41k • written 8.8 years ago by
bharata1803
▴ 60
2
votes
17
replies
2.1k
views
How to reduce the impact of one varaible in Deseq2 or edgeR for multivariate value analysis?
MultipleComparison
edgeR
DESeq2
written 2.0 years ago by
yuet
• 0
22
votes
17
replies
7.0k
views
DESeq2 1.20.0 lfcshrink function
deseq2
differential expression
logfoldchange
lfcshrink
lfcthreshold
updated 2.8 years ago by
Michael Love
41k • written 5.8 years ago by
emi.sch
▴ 30
0
votes
17
replies
3.3k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2
differential expression
error
updated 9 months ago by
snow34
• 0 • written 6.5 years ago by
ap3637
• 0
0
votes
17
replies
2.2k
views
DESeq2 shrunken log fold changes
deseq2
3.9 years ago
dequattro.concetta
▴ 10
2
votes
17
replies
4.0k
views
Multi-factorial design in DEseq2: defining reduced model
deseq2
multifactorial design
reduced model
7.2 years ago
laianavarromartin
▴ 20
2
votes
17
replies
2.8k
views
DESeq2- what to do when two conditions share controls?
deseq2
6.8 years ago
grashow
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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