Showing : DEseq2 • reset
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
9 months ago Anna • 0
1
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2
replies
759
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Deseq2 res Function
DESeq2
updated 9 months ago by 68k • written 10 months ago by ▴ 10
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4
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687
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
10 months ago NB • 0
0
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5
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727
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Identical samples after deseq2 batch effect removal
DESeq2
updated 10 months ago by 43k • written 10 months ago by • 0
0
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1
reply
540
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 10 months ago by 68k • written 10 months ago by • 0
1
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2
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458
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
10 months ago Denise • 0
0
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1
reply
378
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eRNAs count
RNASeq DESeq2
updated 10 months ago by ★ 4.9k • written 10 months ago by • 0
0
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1
reply
583
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DESeq2 rerun returns different results
DESeq2
updated 10 months ago by ★ 4.9k • written 10 months ago by • 0
0
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1
reply
483
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 10 months ago by 43k • written 10 months ago by • 0
0
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1
reply
469
views
DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
2
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2
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1.0k
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Handling biological replicates in DESeq2
DESeq2
updated 10 months ago by ★ 4.9k • written 10 months ago by • 0
5
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3
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29k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.7 years ago by ▴ 30
1
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6
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1.5k
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 10 months ago by 43k • written 10 months ago by ▴ 10
0
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2
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556
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 10 months ago by • 0
4
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5
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1.2k
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
10 months ago LuciaNhu • 0
0
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1
reply
699
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Average expression of genes across replicates
DESeq2
updated 10 months ago by ★ 4.9k • written 10 months ago by • 0
0
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0
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372
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
10 months ago info ▴ 10
0
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11
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2.3k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 5 months ago by • 0 • written 10 months ago by • 0
0
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1
reply
538
views
Deseq to output continous sequencing data
DESeq2
updated 10 months ago by 43k • written 11 months ago by • 0
1
vote
4
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1.3k
views
Adjusted p-values become NA when sub-setting samples
DESeq2
11 months ago • updated 10 months ago txema.heredia • 0
3
votes
3
replies
1.4k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 10 months ago by • 0
0
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2
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700
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 11 months ago by • 0
0
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1
reply
469
views
Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
2
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3
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1.3k
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Analysis of large RNA-Seq Datasets
DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
1
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4
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1.1k
views
DESeq2 - interactions when using factors concatenated into group
DESeq2
11 months ago • updated 10 months ago boczniak767 ▴ 740
0
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1
reply
340
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
11 months ago JY • 0
0
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1
reply
415
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
0
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2
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455
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how to extract expression matrix post deseq2
DESeq2
written 11 months ago by • 0
0
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2
replies
485
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Using Normalized Counts in DESeq2
DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
3
votes
2
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550
views
When running contrasts, does it use normalized read counts?
DESeq2
11 months ago Katherine ▴ 20
0
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1
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387
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How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 11 months ago by ★ 1.4k • written 11 months ago by • 0
3
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4
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1.1k
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
11 months ago Eva ▴ 10
1
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4
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1.2k
views
Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 11 months ago by ★ 4.9k • written 11 months ago by • 0
0
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1
reply
467
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
2
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4
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799
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
11 months ago jihoon.kim.1495 ▴ 10
0
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6
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1.3k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 10 months ago by 43k • written 11 months ago by • 0
5
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4
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925
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 11 months ago by ★ 4.9k • written 11 months ago by • 0
0
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2
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597
views
RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
11 months ago paul.meraner • 0
0
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0
replies
511
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News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
11 months ago • updated 10 months ago info ▴ 10
1
vote
6
replies
1.3k
views
heatmap with batch effect
DESeq2 BatchEffect
written 11 months ago by • 0
0
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2
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652
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
1
vote
1
reply
916
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 11 months ago by 68k • written 11 months ago by • 0
1
vote
1
reply
521
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 11 months ago by ★ 4.9k • written 11 months ago by • 0
1
vote
1
reply
556
views
DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 11 months ago by ★ 4.9k • written 11 months ago by • 0
1
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2
replies
809
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 11 months ago by 43k • written 12 months ago by ▴ 10
0
votes
2
replies
963
views
DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 11 months ago by 43k • written 12 months ago by • 0
1
vote
2
replies
967
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DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2 Bioconductor
updated 11 months ago by 43k • written 12 months ago by ▴ 10
1
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6
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1.6k
views
New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 11 months ago by ★ 4.9k • written 11 months ago by • 0
0
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1
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434
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Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
17
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9
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8.1k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 12 months ago by 68k • written 9.3 years ago by ▴ 10
4,835 results • Page 3 of 97
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Replies
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Also, you never need to use anything but `BiocManager::install` to install any package, which has the beneficial side effect of ensuring th…
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Yes. Your packages have odd Y version numbers (where the version is X.Y.Z). That means they are devel packages (release versions have even …
Comment: GO.db and others package Download failure by Skyler • 0
Am I using Bioc-devel?
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Is there a reason to use Bioc-devel? If not, you should be using the release version (which I am, and which installs `GO.db` without compla…
Comment: GO.db and others package Download failure by Skyler • 0
Hi James, Below I have inserted all of my code. I have run r as an administrator and not as an administrator. I have changed my CRANmirror …
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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