Showing : deseq2 • reset
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How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
4
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12
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2.0k
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DGE with a Continuous Variable
DESeq2 model
updated 18 months ago by 43k • written 18 months ago by • 0
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2
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799
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DESeq2: two conditions two genotypes
DESeq2
18 months ago Rocio • 0
2
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4
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1.3k
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DESeq normalized counts vs CQN and statistics
DESeq2 cqn
written 18 months ago by • 0
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1
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1.1k
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Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 18 months ago by 43k • written 18 months ago by • 0
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1
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672
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unreal negative log2fc values
DESeq2 des
updated 18 months ago by 68k • written 18 months ago by • 0
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1
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585
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LRT test for different timepoints (one tissue types vs. many tissue types)
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
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8
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2.0k
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Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 18 months ago by 53k • written 19 months ago by • 0
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2
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3.5k
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Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment.
DESeq2
19 months ago sropri • 0
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1
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614
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Deseq2 design matrix
DESeq2 Designmatrix limma
updated 19 months ago by 68k • written 19 months ago by • 0
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1
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827
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DESeq2 - vst() - log2FC - no replicates
DESeq2 log2FC vst()
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
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5
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1.2k
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DESeq2 ML Query
DESeq2
updated 18 months ago by 43k • written 19 months ago by • 0
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3
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1.1k
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Test of Multiple Linear Combination on coefficients from Wald Test in Deseq2
Regression DESeq2
19 months ago • updated 17 months ago David W. H. • 0
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1
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772
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 19 months ago by 68k • written 19 months ago by • 0
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3
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2.0k
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
19 months ago Tanvi • 0
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1
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1.4k
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In a 3 group DEG analysis with three batches, can I use 1 group in all three batches to correct for the batch effect?
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
2
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1
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711
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Design formula, numeric contrast, and lfcshrink in deseq2
DESeq2
updated 19 months ago by 43k • written 19 months ago by ▴ 10
2
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1
reply
881
views
DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 19 months ago by 68k • written 19 months ago by ▴ 70
1
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9
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3.7k
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 19 months ago by 68k • written 19 months ago by ▴ 10
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3
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1.1k
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 19 months ago by 68k • written 19 months ago by ▴ 50
3
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6
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3.8k
views
Multiple factor DSEq2 result generates weird volcano plot
DESeq2
updated 19 months ago by ★ 5.0k • written 2.8 years ago by ▴ 20
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2
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991
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Double normalising when using sva and deseq2
DESeq2 Normalisation Bulkrnaseq Svaseq
19 months ago BioinfGuru ▴ 70
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2
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1.4k
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Cohen's D calculation for differentially expressed genes via DESeq2 results summary stats
DESeq2
19 months ago a_p • 0
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1
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765
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Can we compare 3 different experimental conditions with DESeq2?
DESeq2 StatisticalMethod
updated 19 months ago by ★ 1.4k • written 19 months ago by • 0
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1
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691
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How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 19 months ago by 68k • written 19 months ago by • 0
1
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2
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2.9k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 19 months ago by ▴ 40 • written 6.2 years ago by • 0
0
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1
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545
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multiple condition issue running DESeq
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
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3
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787
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Ploting of normalized counts after batch removal
DESeq2
updated 19 months ago by 53k • written 19 months ago by ▴ 10
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1
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518
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makeExampleDESeqDataSet using pilot data
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
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2
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741
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Best way to describe DEseq2 design
DESeq2
updated 19 months ago by ★ 1.4k • written 19 months ago by • 0
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2
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882
views
Deseq2
DESeq2 rnaseqGene
updated 19 months ago by ▴ 220 • written 19 months ago by • 0
1
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1
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605
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LRT, pairwise comparisons and p-value adjustment
DESeq2
updated 19 months ago by 68k • written 20 months ago by ▴ 740
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6
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1.2k
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Counter-directional LFC shrinkage
DESeq2
updated 19 months ago by 43k • written 20 months ago by • 0
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2
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1.3k
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How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat DESeq2 single-cell scRNA Pseudobulk
updated 20 months ago by ★ 4.1k • written 20 months ago by • 0
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3
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2.2k
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GSVA function
DESeq2 GSVA ssGSEA
updated 20 months ago by ★ 3.4k • written 20 months ago by • 0
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2
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1.0k
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
20 months ago sukeshinik5 ▴ 20
0
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4
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2.3k
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Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
1
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8
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1.4k
views
Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
20 months ago boczniak767 ▴ 740
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3
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1.1k
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 20 months ago by 68k • written 20 months ago by ▴ 740
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6
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1.7k
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
20 months ago Ken C • 0
2
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4
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1.2k
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 20 months ago by 43k • written 20 months ago by • 0
4
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9
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1.5k
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
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3
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834
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 20 months ago by 43k • written 20 months ago by • 0
0
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1
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827
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 20 months ago by 43k • written 20 months ago by • 0
0
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9
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2.4k
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 19 months ago by ▴ 70 • written 20 months ago by • 0
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2
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1.2k
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
20 months ago BioinfGuru ▴ 70
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1
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656
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
0
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1
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764
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
2
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7
replies
2.1k
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
20 months ago sajadahmad41454 • 0
2
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1
reply
877
views
Handling multiple differential expression comparisons
DESeq2
20 months ago • updated 19 months ago Zainab ▴ 20
4,844 results • Page 5 of 97
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Comment: Pairwise comparison of multiple groups with different base by ja569116 • 0
Hi @mikelove I have a similar situation, and I feel that I have interpreted the results in the wrong way. In my case I would like to identi…
Comment: Are individual-mouse-based statistics possible in CellChat? by TikTsossakaas33ocissalpc • 0
Questions about comparing groups and statistical significance highlight how data driven thinking matters across fields. In online mobile ga…
Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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