Showing : DESeq2 • reset
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 4 hours ago by 41k • written 1 day ago by ▴ 20
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1
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135
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How to retrieve detailed regression results from deseq2
DESeq2
updated 1 day ago by 41k • written 5 days ago by ▴ 10
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2
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99
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DEG with low counts
DESeq2
updated 1 day ago by 41k • written 1 day ago by • 0
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1
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69
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Deseq2 Rlog transformation
DESeq2
updated 1 day ago by ★ 4.0k • written 2 days ago by • 0
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2
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123
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Design Matrix within group comparison more than two groups
DESeq2
4 days ago • updated 3 days ago hemantcnaik • 0
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1
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91
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Bioinformatics student
Des DESeq2
updated 4 days ago by • 0 • written 4 days ago by • 0
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1
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124
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DESeq2 gives an error and R crashes
DESeq2
5 days ago • updated 4 days ago Shefali • 0
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2
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166
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 6 days ago by 41k • written 11 days ago by ▴ 30
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1
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113
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 6 days ago by 41k • written 7 days ago by • 0
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2
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202
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Regressing out batch effects
DESeq2
updated 6 days ago by 41k • written 12 days ago by • 0
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2
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125
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 11 days ago by 65k • written 11 days ago by • 0
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1
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140
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DESeq2 - Missing values in count matrix
DESeq2
updated 12 days ago by 65k • written 12 days ago by • 0
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6
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383
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 12 days ago by 41k • written 13 days ago by • 0
1
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1
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123
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
14 days ago • updated 13 days ago Layal • 0
0
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2
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138
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
14 days ago • updated 13 days ago michelafrancesconi8 • 0
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4
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205
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 13 days ago by 41k • written 14 days ago by • 0
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1
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129
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 18 days ago by 41k • written 18 days ago by • 0
2
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3
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303
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PCA of different bacterial species
DESeq2
updated 20 days ago by 41k • written 20 days ago by ▴ 10
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1
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145
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collapseReplicates dimension error
DESeq2 Dese
updated 21 days ago by 41k • written 25 days ago by • 0
3
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2
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182
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
22 days ago Anita ▴ 10
1
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2
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195
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
25 days ago • updated 20 days ago Chanderkant Chaudhary • 0
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2
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188
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
26 days ago • updated 25 days ago kcarey • 0
2
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3
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266
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DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 26 days ago by 41k • written 28 days ago by ▴ 20
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3
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222
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Help with Complex DESeq2 Design
DESeq2
updated 27 days ago by ★ 4.0k • written 28 days ago by • 0
1
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1
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150
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Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2 ctsGE
updated 29 days ago by 41k • written 29 days ago by • 0
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1
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122
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Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 29 days ago by 41k • written 29 days ago by • 0
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1
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154
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lfcShrink error: the line search routine failed
apeglm DESeq2
updated 29 days ago by 41k • written 29 days ago by • 0
2
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2
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195
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With DESeq2 "Not full rank" Error with design
DESeq2 DEs
4 weeks ago feather-W • 0
0
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2
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288
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
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4
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395
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DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
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7
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393
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DESeq2 filtering vs edgeR filtering
DESeq2
4 weeks ago • updated 21 days ago fr8712ca-s • 0
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2
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219
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
4 weeks ago kcarey • 0
1
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1
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196
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i'm not getting any differentially expressed genes.
DESeq2
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
2
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1
reply
219
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Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
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1
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188
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Perform PCA for sample clustering using DESeq2
DESeq2
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
0
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3
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348
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 10 weeks ago by • 0
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2
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308
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DESeq2: Comparing A Knockout to a Strain
DESeq2
5 weeks ago Viktor Thiel • 0
0
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1
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190
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DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2 scCITE-seq
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
0
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8
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359
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
5 weeks ago michelafrancesconi8 • 0
0
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1
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193
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Unusually large fold-changes in Deseq2 results
DESeq2
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
1
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4
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277
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DESeq2 Replicates
DESeq2 RNASeq
5 weeks ago kcarey • 0
2
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6
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306
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Factor vs Character in design
DESeq2
5 weeks ago James Aiden • 0
1
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3
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293
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Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2 glmGamPoi
6 weeks ago • updated 5 weeks ago I-Hsuan Lin ▴ 10
4
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7
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821
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weird volcano plot
DESeq2
updated 5 weeks ago by • 0 • written 5 months ago by ▴ 10
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1
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249
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DEseq2 dispersion plot
DESeq2
updated 5 weeks ago by 41k • written 6 weeks ago by • 0
1
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3
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320
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 6 weeks ago by ★ 1.3k • written 6 weeks ago by ▴ 10
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2
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343
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Is DESeq2 normalisation appropriate when counts were obtained for a small number of genes?
DESeq2
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
0
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3
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270
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Would I treat surrogate variables as batches?
DESeq2 sva
updated 6 weeks ago by 65k • written 6 weeks ago by ▴ 10
0
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1
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223
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Changed DESeq2 comparison value but the heatmap is still the same
DESeq2 pheatmap
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
1
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4
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309
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Further clarification of unbalanced group sizes DESeq2
DESeq2
6 weeks ago hmillike • 0
50 results • Page 1 of 1
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Comment: geneList error in clusterprofiler by Ana • 0
Ahh thank you, that fixed it!
Answer: geneList error in clusterprofiler by Basti ▴ 760
Have a look at the documentation : https://www.rdocumentation.org/packages/clusterProfiler/versions/3.0.4/topics/gseGO geneList argument s…
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Answer: geneList error in clusterprofiler
Comment: Memory errors using read.bismark?
Comment: Not fully paired differential gene expression analysis
Comment: [DiffBind] Obtaining normalization factors
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
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