Showing : DEseq2 • reset
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Most sensible approach to a `stage*condition` design in DESeq2
DESeq2
1 hour ago • updated 51 minutes ago alephreish • 0
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16
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What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
2 hours ago BioinfGuru ▴ 30
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1
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38
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LRT test for different timepoints (one tissue types vs. many tissue types)
DESeq2
updated 6 hours ago by 42k • written 12 hours ago by • 0
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6
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285
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Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 4 days ago by 51k • written 6 days ago by • 0
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2
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278
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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
7 days ago • updated 6 days ago sropri • 0
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1
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99
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Deseq2 design matrix
DESeq2 Designmatrix limma
updated 8 days ago by 66k • written 8 days ago by • 0
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1
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131
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DESeq2 - vst() - log2FC - no replicates
DESeq2 log2FC vst()
updated 12 days ago by ★ 4.2k • written 12 days ago by • 0
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3
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194
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DESeq2 ML Query
DESeq2
updated 6 days ago by 42k • written 13 days ago by • 0
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2
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193
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Test of Multiple Linear Combination on coefficients from Wald Test in Deseq2
Regression DESeq2
updated 14 days ago by 66k • written 14 days ago by • 0
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1
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162
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 15 days ago by 66k • written 15 days ago by • 0
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3
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217
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
15 days ago Tanvi • 0
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1
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904
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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 18 days ago by 42k • written 25 days ago by • 0
2
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1
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261
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Design formula, numeric contrast, and lfcshrink in deseq2
DESeq2
updated 19 days ago by 42k • written 25 days ago by ▴ 10
2
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1
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172
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 19 days ago by 66k • written 19 days ago by ▴ 50
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9
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447
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 15 days ago by 66k • written 21 days ago by • 0
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3
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267
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 21 days ago by 66k • written 21 days ago by ▴ 50
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6
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1.8k
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Multiple factor DSEq2 result generates weird volcano plot
DESeq2
updated 21 days ago by ★ 4.2k • written 15 months ago by ▴ 20
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2
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171
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Double normalising when using sva and deseq2
DESeq2 Normalisation Bulkrnaseq Svaseq
23 days ago • updated 22 days ago BioinfGuru ▴ 30
1
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2
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361
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Cohen's D calculation for differentially expressed genes via DESeq2 results summary stats
DESeq2
27 days ago • updated 25 days ago a_p • 0
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1
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153
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Can we compare 3 different experimental conditions with DESeq2?
DESeq2 StatisticalMethod
updated 25 days ago by ★ 1.4k • written 26 days ago by • 0
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1
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155
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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 26 days ago by 66k • written 26 days ago by • 0
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2
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1.9k
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using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 27 days ago by ▴ 40 • written 4.7 years ago by • 0
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1
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174
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multiple condition issue running DESeq
DESeq2
updated 29 days ago by 42k • written 29 days ago by • 0
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3
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269
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Ploting of normalized counts after batch removal
DESeq2
updated 4 weeks ago by 51k • written 4 weeks ago by ▴ 10
1
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1
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164
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makeExampleDESeqDataSet using pilot data
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
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2
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202
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Best way to describe DEseq2 design
DESeq2
updated 4 weeks ago by ★ 1.4k • written 4 weeks ago by • 0
1
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2
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236
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Deseq2
DESeq2 rnaseqGene
updated 4 weeks ago by ▴ 210 • written 4 weeks ago by • 0
1
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1
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188
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LRT, pairwise comparisons and p-value adjustment
DESeq2
updated 4 weeks ago by 66k • written 5 weeks ago by ▴ 740
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6
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403
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Counter-directional LFC shrinkage
DESeq2
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
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2
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251
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How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat DESeq2 single-cell scRNA Pseudobulk
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
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3
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309
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GSVA function
DESeq2 GSVA ssGSEA
updated 5 weeks ago by ★ 3.3k • written 5 weeks ago by • 0
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2
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234
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
5 weeks ago sukeshinik5 • 0
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4
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460
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Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 5 weeks ago by ★ 4.2k • written 5 weeks ago by • 0
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8
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355
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Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
6 weeks ago • updated 5 weeks ago boczniak767 ▴ 740
1
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3
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292
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 6 weeks ago by 66k • written 6 weeks ago by ▴ 740
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6
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757
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
6 weeks ago Ken C • 0
2
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4
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349
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
4
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9
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441
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 6 weeks ago by ★ 4.2k • written 7 weeks ago by • 0
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3
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224
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
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1
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180
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
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9
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864
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 4 weeks ago by ▴ 30 • written 7 weeks ago by • 0
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2
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349
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
7 weeks ago • updated 6 weeks ago BioinfGuru ▴ 30
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1
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248
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 7 weeks ago by ★ 4.2k • written 7 weeks ago by • 0
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1
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178
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 7 weeks ago by ★ 4.2k • written 7 weeks ago by • 0
2
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7
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600
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
8 weeks ago • updated 7 weeks ago sajadahmad41454 • 0
2
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1
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314
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Handling multiple differential expression comparisons
DESeq2
8 weeks ago • updated 20 days ago Zainab ▴ 10
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6
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412
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 8 weeks ago by ★ 1.4k • written 8 weeks ago by ▴ 130
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5
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446
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 9 days ago by ★ 4.2k • written 8 weeks ago by • 0
0
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2
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230
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DESeq2 v1.35.0
DESeq2
updated 8 weeks ago by 42k • written 8 weeks ago by • 0
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2
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292
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Deseq2 and Normalization of RNA sequencing data
DESeq2
8 weeks ago kcarey • 0
50 results • Page 1 of 1
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Comment: Trouble Installing DADA2 (warning: R new user) by shepherl 3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
Answer: LRT test for different timepoints (one tissue types vs. many tissue types) by Michael Love 42k
No, this is a contrast of estimated coefficient (e.g. the Wald test).
Comment: Ranking the GSEA Results by Michael Love 42k
Got it. So then I'll take off DESeq2 as its mostly a downstream question. You may need to direct the fgsea developer to the thread. When yo…
Comment: Ranking the GSEA Results by V_Vibes • 0
I have actually used the "fgsea" Bioconductor package which is used for GSEA. Thanks for pointing that out. I have edited that in the origi…
Comment: Ranking the GSEA Results by V_Vibes • 0
The idea was inspired by people ranking the DEGs for preranked GSEA using their log2FC * (-log10 p-value). Also, the GSEA results I am gett…
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Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
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