Showing : DESeq2 • reset
16
votes
40
replies
5.0k
views
Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 13 months ago by • 0 • written 3.5 years ago by ▴ 50
5
votes
27
replies
2.7k
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 2.1 years ago by 39k • written 5.6 years ago by ▴ 10
1
vote
26
replies
4.1k
views
How can I install DeSeq2 in Jupyter Notebook?
deseq2
updated 4.0 years ago by ▴ 70 • written 4.0 years ago by ▴ 20
0
votes
25
replies
1.9k
views
deseq2 course experiment
deseq2
5.7 years ago ribioinfo ▴ 100
18
votes
24
replies
12k
views
[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 24 months ago by • 0 • written 7.9 years ago by ▴ 120
10
votes
23
replies
9.7k
views
Macbook M1 install genefilter failed
DESeq2 m1 macbook genefilter
18 months ago • updated 3 months ago soda ▴ 80
2
votes
23
replies
2.5k
views
Coping with a label/class imbalance in DESeq2
deseq2 rnaseq r regression
updated 6.4 years ago by 39k • written 6.4 years ago by • 0
24
votes
22
replies
15k
views
DESeq2 for ChIP-seq differential peaks
deseq2 deseq chipseq
updated 5.6 years ago by ▴ 120 • written 7.4 years ago by ▴ 190
1
vote
22
replies
4.1k
views
DESeq2 for Ribosomal profiling analysis
deseq2
6.9 years ago • updated 6.8 years ago jxu006 ▴ 10
1
vote
22
replies
3.5k
views
DESEq2 Large Memory When Parallel
deseq2
updated 5.3 years ago by 39k • written 5.3 years ago by ▴ 10
4
votes
21
replies
8.7k
views
DESeq2 and ComBat
deseq2 combat
updated 7.1 years ago by ▴ 600 • written 7.1 years ago by ▴ 100
32
votes
21
replies
11k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
8.4 years ago • updated 4 months ago Michael Love 39k
0
votes
20
replies
1.3k
views
DESeq2 question: why I got discrepancy results for DEGs when using different ways setting up the models
DESeq2 DEGs
19 months ago • updated 18 months ago Ming ▴ 360
1
vote
20
replies
951
views
Deseq2 installed, but there is no package called ‘Biostrings’
DESeq2 Install
updated 3 months ago by 62k • written 3 months ago by • 0
2
votes
20
replies
1.4k
views
plotPCA in DESeq2
software error deseq2
2.6 years ago yueli7 ▴ 20
51
votes
20
replies
35k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 6.7 years ago by • 0 • written 7.1 years ago by ▴ 110
8
votes
20
replies
19k
views
DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 11 weeks ago by ▴ 10 • written 6.6 years ago by ▴ 20
0
votes
20
replies
1000
views
Different DESeq2 results (both FC and pvalue) by changing col/row orders in input
DESeq2
7 months ago Weisheng • 0
14
votes
19
replies
8.0k
views
DESeq2 Model Design
DESeq2 linear model model
updated 21 months ago by 39k • written 8.2 years ago by ▴ 360
14
votes
19
replies
16k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
updated 12 months ago by ▴ 50 • written 8.3 years ago by ▴ 120
3
votes
19
replies
4.5k
views
lfcShrink and factors with multiple levels
deseq2 lfcshrink relevel
updated 5.2 years ago by 39k • written 5.2 years ago by ▴ 80
0
votes
19
replies
1.2k
views
Paired Difference Analysis
deseq2 R differential gene expression
5.5 years ago • updated 5.4 years ago nhua • 0
6
votes
19
replies
2.5k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 5.4 years ago by ▴ 660 • written 5.4 years ago by ▴ 50
5
votes
18
replies
1.0k
views
Difference of difference, paired design
edger deseq2 limma
updated 3.6 years ago by ★ 1.2k • written 3.6 years ago by • 0
0
votes
18
replies
1.4k
views
Subset-ing Large DESeqDataSet for data extraction with contrast function
deseq2
updated 3.4 years ago by 39k • written 3.4 years ago by • 0
5
votes
18
replies
1.3k
views
DESeq2 comparison two cell types and two genotypes
GeneExpressionWorkflow DESeq2 GeneExpression
updated 21 months ago by 39k • written 21 months ago by • 0
8
votes
18
replies
8.3k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 24 months ago by • 0 • written 3.3 years ago by ▴ 10
0
votes
18
replies
3.7k
views
DEseq2 metagenomic analysis without replicates
DESeq2 DESeq2
updated 9.1 years ago by ▴ 220 • written 9.1 years ago by ★ 12k
3
votes
18
replies
2.4k
views
DESeq2 filter out my expression gene
deseq2
updated 7.0 years ago by 39k • written 7.0 years ago by ▴ 40
0
votes
18
replies
2.1k
views
DESeq2 in R_devel: a bug?
DESeq2 DESeq2
updated 8.9 years ago by 39k • written 8.9 years ago by ▴ 80
9
votes
18
replies
2.3k
views
What is the correct use of removeBatchEffect's design parameter
deseq2 limma
updated 23 months ago by 47k • written 2.4 years ago by ▴ 10
15
votes
18
replies
1.2k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 10 months ago by 47k • written 10 months ago by ▴ 60
6
votes
18
replies
10k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
3.7 years ago Mozart ▴ 20
1
vote
18
replies
3.1k
views
DESEQ2 linear model of dose
deseq2
updated 6.3 years ago by ★ 3.7k • written 6.3 years ago by ▴ 10
0
votes
18
replies
1.8k
views
DESeq2: Possible issue with colData and sorting
deseq2 summarizedexperiment
updated 6.4 years ago by 25k • written 6.4 years ago by ▴ 40
4
votes
18
replies
20k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 3.6 years ago by • 0 • written 8.3 years ago by ▴ 100
4
votes
18
replies
2.7k
views
DESeq2 - multifactorial design
LRT DESeq2 interaction
updated 22 months ago by 3.7k • written 23 months ago by ▴ 10
7
votes
17
replies
4.5k
views
DESeqDataSetFromTximport: Error in checkSlotAssignment
deseq2 tximport
5.8 years ago JWCarlson ▴ 80
9
votes
17
replies
1.1k
views
DESeq2 design subcategories
deseq2 deseq differential binding analysis
updated 5.2 years ago by 39k • written 5.2 years ago by ▴ 60
4
votes
17
replies
4.0k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor Install DESeq2
updated 11 weeks ago by 39k • written 12 months ago by • 0
0
votes
17
replies
6.2k
views
DESeq2 Error NA values
deseq2
updated 7.7 years ago by 39k • written 7.7 years ago by ▴ 40
2
votes
17
replies
1.1k
views
How to reduce the impact of one varaible in Deseq2 or edgeR for multivariate value analysis?
MultipleComparison edgeR DESeq2
written 10 months ago by • 0
2
votes
17
replies
1.2k
views
Computationally Singular Matrices - DESeq
deseq2 rnaseq sva
updated 3 months ago by 39k • written 3.9 years ago by • 0
2
votes
17
replies
3.1k
views
Multi-factorial design in DEseq2: defining reduced model
deseq2 multifactorial design reduced model
6.0 years ago laianavarromartin ▴ 20
2
votes
17
replies
2.2k
views
DESeq2- what to do when two conditions share controls?
deseq2
5.7 years ago grashow ▴ 10
0
votes
17
replies
1.2k
views
DESeq2 shrunken log fold changes
deseq2
2.8 years ago dequattro.concetta ▴ 10
0
votes
17
replies
1.7k
views
DESeq2 : NA p values reported
DESeq2 DESeq2
updated 9.2 years ago by ▴ 420 • written 9.2 years ago by ▴ 160
21
votes
17
replies
5.2k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 20 months ago by 39k • written 4.6 years ago by ▴ 20
3
votes
16
replies
1.4k
views
DESeq2 interaction term
DESeq2
5.0 years ago Catalina Aguilar Hurtado ▴ 80
30
votes
16
replies
14k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 4.8 years ago by ▴ 20 • written 6.6 years ago by ▴ 190
50 results • Page 1 of 1
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Replies
Comment: TCGA: clinical data and expression data by sharifnstu1203002m • 0
Hello, I am in the same problem. I downloaded "transcriptome profiling" data of TCGA by using the Bioconductor package. I get my gene expr…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Jonathan Göke ▴ 40
Great to hear that you are using Bambu. Yes, I think that part of your question does not have one correct answer, there are many ways in wh…
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R by Gordon Smyth 47k
Choosing which samples to normalize together is not dependent on library size but rather on (1) whether the tissue samples are comparable a…
Comment: Atena package - error (new user) by lalanis1 • 0
Thanks a lot, Calvo. Will run my files with revised version soon! Best regards, Lalani
Comment: Nested paired design with covariates in limma by Gordon Smyth 47k
Please post a new question with enough detail to answer your question. If you want bespoke advance, then you need to post the details of yo…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
C: Can't install TopmedPipeline Package
Comment: Question about GWASTools gdsSubset
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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