Showing : DESeq2 • reset
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Best way to describe DEseq2 design
DESeq2
updated 3 hours ago by ▴ 350 • written 4 hours ago by • 0
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Deseq2
DESeq2 rnaseqGene
updated 1 hour ago by ▴ 210 • written 5 hours ago by • 0
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LRT, pairwise comparisons and p-value adjustment
DESeq2
updated 1 day ago by 66k • written 2 days ago by ▴ 720
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6
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171
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Counter-directional LFC shrinkage
DESeq2
updated 6 hours ago by 42k • written 2 days ago by • 0
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2
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130
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How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat DESeq2 single-cell scRNA Pseudobulk
updated 3 days ago by ★ 4.0k • written 4 days ago by • 0
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3
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GSVA function
DESeq2 GSVA ssGSEA
updated 3 days ago by ★ 3.3k • written 6 days ago by • 0
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124
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
6 days ago • updated 3 days ago sukeshinik5 • 0
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4
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261
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Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 4 days ago by ★ 4.2k • written 6 days ago by • 0
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8
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206
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Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
8 days ago • updated 7 days ago boczniak767 ▴ 720
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 10 days ago by 66k • written 11 days ago by ▴ 720
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
13 days ago • updated 10 days ago Ken C • 0
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 10 days ago by 42k • written 13 days ago by • 0
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9
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345
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 14 days ago by ★ 4.2k • written 15 days ago by • 0
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175
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 15 days ago by 42k • written 16 days ago by • 0
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134
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 16 days ago by 42k • written 17 days ago by • 0
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 15 days ago by ▴ 30 • written 17 days ago by • 0
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
16 days ago • updated 14 days ago BioinfGuru ▴ 30
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 20 days ago by ★ 4.2k • written 20 days ago by • 0
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128
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 21 days ago by ★ 4.2k • written 21 days ago by • 0
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
22 days ago • updated 19 days ago sajadahmad41454 • 0
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205
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Handling multiple differential expression comparisons
DESeq2
updated 25 days ago by 42k • written 27 days ago by ▴ 10
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327
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 26 days ago by ★ 1.4k • written 27 days ago by ▴ 130
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 25 days ago by ★ 4.2k • written 27 days ago by • 0
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189
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DESeq2 v1.35.0
DESeq2
updated 28 days ago by 42k • written 28 days ago by • 0
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Deseq2 and Normalization of RNA sequencing data
DESeq2
28 days ago • updated 27 days ago kcarey • 0
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255
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 28 days ago by ★ 4.2k • written 28 days ago by • 0
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3
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345
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Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 22 days ago by ★ 4.2k • written 28 days ago by • 0
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3
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319
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 28 days ago by 42k • written 29 days ago by • 0
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172
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
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189
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
4 weeks ago • updated 27 days ago Aurora • 0
0
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148
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
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149
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putting my own expression data in deseq2
DESeq2
updated 4 weeks ago by ★ 4.2k • written 4 weeks ago by • 0
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 4 weeks ago by ★ 4.2k • written 4 weeks ago by ▴ 10
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PCA plot suggestions
DESeq2 PCAtools
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
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270
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 5 weeks ago by 66k • written 5 weeks ago by • 0
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182
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
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255
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Different Shrunk Log2FC according with reference
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by ▴ 20
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4
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377
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
5 weeks ago • updated 4 weeks ago winwater0928 • 0
3
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350
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by ▴ 40
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 5 weeks ago by ★ 1.4k • written 5 weeks ago by • 0
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3
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276
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
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167
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rlog transformation
DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
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144
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
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797
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
6 weeks ago • updated 4 weeks ago Patadù ▴ 10
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156
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covariate with negative and positive values
DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
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1
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178
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 6 weeks ago by ★ 4.2k • written 6 weeks ago by • 0
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4
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288
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
6 weeks ago • updated 5 weeks ago lonn • 0
0
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3
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241
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by ▴ 20
1
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2
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281
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How to retrieve detailed regression results from deseq2
DESeq2
7 weeks ago • updated 5 weeks ago Weiqian ▴ 10
50 results • Page 1 of 1
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Comment: Deseq2 by Ram ▴ 210
Cross-posted on biostars: https://www.biostars.org/p/9596031/
Comment: SpliceWiz collateData error by giulia.nicoletto.1 • 0
Hi there, I am facing a similar error. When I try the collateData command collateData( Experiment = expr, reference_path = "./Referen…
Answer: Best way to describe DEseq2 design by SamGG ▴ 350
Hi, My own opinion. In the design `~ Batch`, ChemicalA_t1 is the intercept. So, all coefficients refer to this level as a reference. …
Answer: Deseq2 by ATpoint ★ 4.2k
Ser the vignette https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html It covers prefiltering (and everyt…
Comment: Counter-directional LFC shrinkage by Michael Love 42k
Gene 1 is hard to predict given the paucity of data for the comparison of interest. What is happening is that the relatively low dispersion…
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Answer: Deseq2
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: When should I correct for batch effects
Answer: When should I correct for batch effects
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