Showing : DeSeq2 • reset
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Doubt about model in paired samples (intercept ?)
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
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10
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2.2k
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Two treatments, one control
DESeq2 stageR
19 months ago • updated 18 months ago alephreish • 0
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2
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2.1k
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How to correct for a covariate in DESeq2 that is linear with the condition of interest
DESeq2
18 months ago Fiona • 0
2
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3
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1.0k
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DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 18 months ago by • 0
0
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1
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1.2k
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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
1
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2
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818
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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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1.4k
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DESeq normalized counts vs CQN and statistics
DESeq2 cqn
written 18 months ago by • 0
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 19 months ago by • 0
0
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1
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681
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unreal negative log2fc values
DESeq2 des
updated 19 months ago by 68k • written 19 months ago by • 0
0
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1
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601
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LRT test for different timepoints (one tissue types vs. many tissue types)
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
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8
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2.1k
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Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 19 months ago by 53k • written 19 months ago by • 0
1
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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
0
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1
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622
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Deseq2 design matrix
DESeq2 Designmatrix limma
updated 19 months ago by 68k • written 19 months ago by • 0
1
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1
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841
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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 18 months ago David W. H. • 0
0
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1
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790
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 19 months ago by 68k • written 19 months ago by • 0
1
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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
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 20 months ago by • 0
2
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1
reply
716
views
Design formula, numeric contrast, and lfcshrink in deseq2
DESeq2
updated 19 months ago by 43k • written 20 months ago by ▴ 10
2
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1
reply
909
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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4.0k
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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
1
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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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3.9k
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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1.0k
views
Double normalising when using sva and deseq2
DESeq2 Normalisation Bulkrnaseq Svaseq
20 months ago BioinfGuru ▴ 70
1
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2
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1.4k
views
Cohen's D calculation for differentially expressed genes via DESeq2 results summary stats
DESeq2
20 months ago a_p • 0
0
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1
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773
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Can we compare 3 different experimental conditions with DESeq2?
DESeq2 StatisticalMethod
updated 20 months ago by ★ 1.4k • written 20 months ago by • 0
0
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1
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705
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 20 months ago by 68k • written 20 months ago by • 0
1
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2
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3.0k
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using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 20 months ago by ▴ 40 • written 6.3 years ago by • 0
0
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1
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557
views
multiple condition issue running DESeq
DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
0
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3
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804
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Ploting of normalized counts after batch removal
DESeq2
updated 20 months ago by 53k • written 20 months ago by ▴ 10
1
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1
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533
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makeExampleDESeqDataSet using pilot data
DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
0
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2
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755
views
Best way to describe DEseq2 design
DESeq2
updated 20 months ago by ★ 1.4k • written 20 months ago by • 0
1
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2
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896
views
Deseq2
DESeq2 rnaseqGene
updated 20 months ago by ▴ 220 • written 20 months ago by • 0
1
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1
reply
616
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LRT, pairwise comparisons and p-value adjustment
DESeq2
updated 20 months ago by 68k • written 20 months ago by ▴ 740
0
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6
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1.2k
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Counter-directional LFC shrinkage
DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
0
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2
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1.4k
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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
0
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3
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2.3k
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GSVA function
DESeq2 GSVA ssGSEA
updated 20 months ago by ★ 3.4k • written 20 months ago by • 0
0
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2
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1.1k
views
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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2.4k
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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
1
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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
views
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
0
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3
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846
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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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846
views
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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2.5k
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 20 months ago by ▴ 70 • written 20 months ago by • 0
1
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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
4,848 results • Page 5 of 97
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Comment: msmsTests, inconsistent sign between lFC.Av and LogFC by Ben • 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis by James W. MacDonald 68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by varying.mastodon.isyn • 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error by ansley.r.burtch • 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Votes
A: DESeq2 - VST eliminates zero values
Comment: Normalise to a housekeeping gene in DESEq2
Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
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