Showing : DESeq2 • reset
16
votes
40
replies
3.0k
views
Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 14 days ago by • 0 • written 2.5 years ago by ▴ 50
5
votes
27
replies
2.1k
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 13 months ago by 35k • written 4.6 years ago by ▴ 10
1
vote
26
replies
2.9k
views
How can I install DeSeq2 in Jupyter Notebook?
deseq2
updated 2.9 years ago by ▴ 70 • written 2.9 years ago by ▴ 20
0
votes
25
replies
1.5k
views
deseq2 course experiment
deseq2
4.7 years ago • updated 4.6 years ago ribioinfo ▴ 100
18
votes
24
replies
11k
views
[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 11 months ago by • 0 • written 6.9 years ago by ▴ 110
2
votes
23
replies
1.9k
views
Coping with a label/class imbalance in DESeq2
deseq2 rnaseq r regression
updated 5.3 years ago by 35k • written 5.3 years ago by • 0
1
vote
22
replies
2.9k
views
DESEq2 Large Memory When Parallel
deseq2
updated 4.2 years ago by 35k • written 4.2 years ago by ▴ 10
1
vote
22
replies
3.5k
views
DESeq2 for Ribosomal profiling analysis
deseq2
5.8 years ago jxu006 ▴ 10
23
votes
22
replies
12k
views
DESeq2 for ChIP-seq differential peaks
deseq2 deseq chipseq
updated 4.6 years ago by ▴ 100 • written 6.4 years ago by ▴ 170
4
votes
21
replies
7.8k
views
DESeq2 and ComBat
deseq2 combat
updated 6.0 years ago by ▴ 600 • written 6.0 years ago by ▴ 100
45
votes
20
replies
28k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 5.6 years ago by • 0 • written 6.1 years ago by ▴ 100
0
votes
20
replies
792
views
DESeq2 question: why I got discrepancy results for DEGs when using different ways setting up the models
DESeq2 DEGs
6 months ago • updated 5 months ago Ming ▴ 360
2
votes
20
replies
675
views
plotPCA in DESeq2
software error deseq2
19 months ago yueli7 ▴ 10
14
votes
19
replies
7.5k
views
DESeq2 Model Design
DESeq2 linear model model
updated 8 months ago by 35k • written 7.2 years ago by ▴ 360
6
votes
19
replies
2.1k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 4.3 years ago by ▴ 590 • written 4.3 years ago by ▴ 50
0
votes
19
replies
1.0k
views
Paired Difference Analysis
deseq2 R differential gene expression
4.4 years ago • updated 4.3 years ago nhua • 0
10
votes
19
replies
3.1k
views
Macbook M1 install genefilter failed
DESeq2 m1 macbook genefilter
updated 8 weeks ago by ▴ 10 • written 5 months ago by ▴ 80
3
votes
19
replies
3.8k
views
lfcShrink and factors with multiple levels
deseq2 lfcshrink relevel
updated 4.2 years ago by 35k • written 4.2 years ago by ▴ 80
0
votes
18
replies
1.8k
views
DESeq2 in R_devel: a bug?
DESeq2 DESeq2
updated 7.9 years ago by 35k • written 7.9 years ago by ▴ 80
8
votes
18
replies
5.7k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 11 months ago by • 0 • written 2.3 years ago by ▴ 10
5
votes
18
replies
750
views
Difference of difference, paired design
edger deseq2 limma
updated 2.5 years ago by ▴ 970 • written 2.5 years ago by • 0
0
votes
18
replies
855
views
Subset-ing Large DESeqDataSet for data extraction with contrast function
deseq2
updated 2.4 years ago by 35k • written 2.4 years ago by • 0
4
votes
18
replies
932
views
DESeq2 - multifactorial design
LRT DESeq2 interaction
updated 10 months ago by 3.4k • written 10 months ago by ▴ 10
1
vote
18
replies
2.5k
views
DESEQ2 linear model of dose
deseq2
updated 5.3 years ago by ★ 3.7k • written 5.3 years ago by ▴ 10
0
votes
18
replies
3.3k
views
DEseq2 metagenomic analysis without replicates
DESeq2 DESeq2
updated 8.0 years ago by ▴ 220 • written 8.0 years ago by ★ 12k
3
votes
18
replies
2.1k
views
DESeq2 filter out my expression gene
deseq2
updated 5.9 years ago by 35k • written 6.0 years ago by ▴ 40
5
votes
18
replies
804
views
DESeq2 comparison two cell types and two genotypes
GeneExpressionWorkflow DESeq2 GeneExpression
updated 8 months ago by 35k • written 8 months ago by • 0
0
votes
18
replies
1.5k
views
DESeq2: Possible issue with colData and sorting
deseq2 summarizedexperiment
updated 5.3 years ago by 25k • written 5.3 years ago by ▴ 40
6
votes
18
replies
7.2k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
2.7 years ago • updated 2.6 years ago Mozart ▴ 20
2
votes
18
replies
18k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 2.6 years ago by • 0 • written 7.2 years ago by ▴ 90
9
votes
18
replies
1.3k
views
What is the correct use of removeBatchEffect's design parameter
deseq2 limma
updated 10 months ago by 44k • written 16 months ago by ▴ 10
6
votes
17
replies
3.8k
views
DESeqDataSetFromTximport: Error in checkSlotAssignment
deseq2 tximport
4.7 years ago JWCarlson ▴ 70
0
votes
17
replies
534
views
DESeq2 shrunken log fold changes
deseq2
21 months ago dequattro.concetta ▴ 10
9
votes
17
replies
834
views
DESeq2 design subcategories
deseq2 deseq differential binding analysis
updated 4.1 years ago by 35k • written 4.1 years ago by ▴ 60
11
votes
17
replies
13k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
written 7.2 years ago by ▴ 120
2
votes
17
replies
1.7k
views
DESeq2- what to do when two conditions share controls?
deseq2
4.7 years ago • updated 4.6 years ago grashow • 0
28
votes
17
replies
9.1k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
7.3 years ago • updated 5.8 years ago Michael Love 35k
2
votes
17
replies
2.5k
views
Multi-factorial design in DEseq2: defining reduced model
deseq2 multifactorial design reduced model
5.0 years ago laianavarromartin ▴ 20
17
votes
17
replies
3.5k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 7 months ago by 35k • written 3.6 years ago by ▴ 20
0
votes
17
replies
5.2k
views
DESeq2 Error NA values
deseq2
updated 6.6 years ago by 35k • written 6.6 years ago by ▴ 40
0
votes
17
replies
1.4k
views
DESeq2 : NA p values reported
DESeq2 DESeq2
updated 8.2 years ago by ▴ 410 • written 8.2 years ago by ▴ 160
0
votes
16
replies
955
views
DESeq2 interaction term
DESeq2
3.9 years ago Catalina Aguilar Hurtado ▴ 70
2
votes
16
replies
2.5k
views
Approaches to group the RNA-Seq samples with large heterogeneity
clustering pca deseq2 edger logfoldchange
updated 5.9 years ago by 35k • written 5.9 years ago by ▴ 10
3
votes
16
replies
1.4k
views
How to add pseudocount to DESeq2 dds object
deseq2 r
updated 11 weeks ago by ▴ 10 • written 16 months ago by • 0
27
votes
16
replies
11k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 3.7 years ago by ▴ 10 • written 5.5 years ago by ▴ 170
4
votes
16
replies
786
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 2.6 years ago by 35k • written 2.6 years ago by ▴ 10
13
votes
16
replies
3.4k
views
Using edgeR or DESeq2 to analyze allele-specific expression?
edgeR deseq2 ase allele
6.3 years ago trianglescout ▴ 40
1
vote
15
replies
3.0k
views
DEseq for chip-seq data normalisation
DESeq DESeq2 DESeq DESeq2
updated 8.2 years ago by ▴ 90 • written 8.2 years ago by ▴ 170
0
votes
15
replies
1.1k
views
Phyloseq to deseq2
deseq2
updated 2.9 years ago by 35k • written 2.9 years ago by • 0
7
votes
15
replies
14k
views
DESEq2 Paired samples Before and after treatment
deseq2 paired samples
5.6 years ago adesrichard ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Answer: Unusal standard deviation after rlog transformation and the homoscedasticity of by Michael Love 35k
I'm guessing this data does not conform well to the assumptions of the rlog, which are that variation is distributed a certain way from exp…
Answer: Affymetrix chip which is not listed on this webpage by James W. MacDonald 58k
You can't use the `affy` package for Clariom S arrays, but instead have to use the `oligo` package. I don't believe `affylmGUI` uses `oligo…
Comment: deseq2 + filtering low counts with noiseq function by Michael Love 35k
Nothing especially concerning about nonparametric methods in my opinion, except that with very low sample size they lose sensitivity. E.g. …
Comment: Using DiffBind blacklists and greylists with results mapped to BDGP6 by Rory Stark ★ 4.3k
I've checked in a fix that should handle this warning condition, it is active in the currently downloadable version if you do a `BiocManage…
Answer: How to get all possible comparisons in DiffBind by Rory Stark ★ 4.3k
Note that contrasts are handled differently since `DiffBind_3.0`. You can still calculate results for multiple contrasts simultaneously, bu…
Votes
A: How to get all possible comparisons in DiffBind
Answer: Limma prametrization
Comment: Limma prametrization
A: Use of pseudoalignment estimated counts as input to edgeR and Limma-Voom
Answer: Unable to GetGRangesFromEnsDb
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