Showing : DESeq2 • reset
38
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23
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17k
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DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
10.6 years ago • updated 5 weeks ago Michael Love 43k
34
votes
29
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16k
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[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 7 months ago by 43k • written 10.1 years ago by ▴ 130
17
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9
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7.6k
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How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 7 months ago by 68k • written 8.9 years ago by ▴ 10
17
votes
11
replies
40k
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DESeq2 and shrinkage of log2 fold changes
deseq2
updated 10 months ago by 43k • written 9.3 years ago by ▴ 100
16
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12
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8.6k
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Diffbind: edgeR or DESeq2 ?
diffbind medip-seq edger deseq2
updated 7 months ago by • 0 • written 9.1 years ago by ▴ 60
10
votes
20
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24k
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Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
updated 6 months ago by 68k • written 5.9 years ago by ▴ 30
8
votes
5
replies
7.8k
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Understanding interaction term in DESeq2
deseq2 design formula log fold change
updated 8 months ago by 43k • written 4.7 years ago by ▴ 40
8
votes
9
replies
15k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 6 hours ago by • 0 • written 8.7 years ago by ▴ 20
6
votes
15
replies
1.9k
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Deseq2 design formula and analysis with internal controls
DESeq2
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
6
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19
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4.8k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 12 months ago by • 0 • written 5.6 years ago by ▴ 10
6
votes
5
replies
3.2k
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What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 3 months ago by ▴ 20 • written 8 months ago by • 0
6
votes
3
replies
7.0k
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DESeq2 with proteomics data
deseq2
updated 7 months ago by 43k • written 6.8 years ago by ▴ 10
5
votes
3
replies
2.2k
views
DeSeq2 Comparing One group vs Two groups
DESeq2
written 3.5 years ago by ▴ 10
5
votes
30
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5.9k
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 25 days ago by • 0 • written 7.8 years ago by ▴ 10
5
votes
4
replies
741
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 6 months ago by ★ 4.8k • written 6 months ago by • 0
5
votes
3
replies
28k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.3 years ago by ▴ 30
4
votes
2
replies
649
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 4 months ago by ★ 4.8k • written 4 months ago by ▴ 10
4
votes
11
replies
1.1k
views
Size factor normalized counts for between sample comparisons - correct?
DESeq2
8 months ago • updated 7 months ago boczniak767 ▴ 740
4
votes
7
replies
1.8k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 8 months ago by ▴ 10 • written 9 months ago by ▴ 70
4
votes
3
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1.4k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 9 months ago by ▴ 10
4
votes
6
replies
1.2k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 28 days ago by ★ 4.8k • written 7 weeks ago by • 0
4
votes
5
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2.0k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2 Dese DifferentialRegulation differe
updated 10 months ago by • 0 • written 2.1 years ago by ▴ 10
4
votes
9
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1.0k
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 11 months ago by ★ 4.8k • written 11 months ago by • 0
4
votes
9
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1.8k
views
DESeq2 unable to handle large count values
DESeq2
updated 6 months ago by 43k • written 17 months ago by • 0
4
votes
5
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971
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
5 months ago LuciaNhu • 0
4
votes
12
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1.4k
views
DGE with a Continuous Variable
DESeq2 model
updated 9 months ago by 43k • written 9 months ago by • 0
3
votes
11
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1.1k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 6 months ago by • 0
3
votes
3
replies
1.2k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 6 months ago by • 0
3
votes
7
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2.1k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 8 weeks ago by ▴ 10 • written 6.1 years ago by ▴ 20
3
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6
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1.0k
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 9 months ago by • 0
3
votes
5
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1.8k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
3
votes
1
reply
703
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 12 months ago by 43k • written 12 months ago by ▴ 10
3
votes
6
replies
30k
views
Deseq: What does "BaseMean" mean?
deseq2
written 6.6 years ago by • 0
3
votes
5
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3.4k
views
Plot PC1 and PC4 in plotPCA function
DESeq2 plotPCA
updated 10 months ago by • 0 • written 3.2 years ago by • 0
3
votes
3
replies
880
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 12 months ago by ★ 4.8k • written 12 months ago by ▴ 10
3
votes
6
replies
3.1k
views
Multiple factor DSEq2 result generates weird volcano plot
DESeq2
updated 10 months ago by ★ 4.8k • written 2.1 years ago by ▴ 20
3
votes
4
replies
2.3k
views
How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
updated 9 weeks ago by • 0 • written 2.9 years ago by ▴ 20
3
votes
4
replies
867
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
6 months ago Eva ▴ 10
3
votes
3
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1.2k
views
the count matrix have decimal values
DESeq2 DifferentialExpression
updated 8 months ago by 68k • written 8 months ago by • 0
3
votes
6
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1.7k
views
[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 7 months ago by 43k • written 7 months ago by • 0
3
votes
4
replies
674
views
Gene filtering in DESeq2
DESeq2
updated 8 months ago by ★ 4.8k • written 8 months ago by • 0
2
votes
7
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2.2k
views
DeSeq2 - Can't fetch any results: Error in .wrap_in_length_one_list_like_object(value, name, x)
deseq2 software error
updated 5 months ago by • 0 • written 5.4 years ago by ▴ 30
2
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3
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2.3k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
updated 2 days ago by • 0 • written 2.5 years ago by ▴ 50
2
votes
4
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1.1k
views
PCA of different bacterial species
DESeq2
written 13 months ago by ▴ 10
2
votes
3
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824
views
Comparing one group against multiple groups in DESeq2
DESeq2
written 15 months ago by • 0
2
votes
1
reply
1.1k
views
DESeq2 time course using fitted splines
RNASeqData TimeCourse DESeq2 timecoursedata
updated 10 months ago by 43k • written 21 months ago by • 0
2
votes
1
reply
1.2k
views
DESeq2 is it OK to scale transformed data in order to plot heatmaps?
DESeq2 heatmaps
updated 8 months ago by ★ 4.8k • written 8 months ago by • 0
2
votes
4
replies
617
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
6 months ago jihoon.kim.1495 ▴ 10
2
votes
9
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1.2k
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
3 months ago Quang NN ▴ 10
2
votes
3
replies
5.0k
views
Deseq2 use fpkm
deseq2
updated 10 months ago by 43k • written 8.5 years ago by ▴ 40
50 results • Page 1 of 1
Recent ...
Replies
Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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