Showing : Deseq2 • reset
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DESeq2 - dispersion estimation when there is none
DESeq2
18 hours ago • updated 3 hours ago WardDeb • 0
0
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1
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78
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rlog transformation
DESeq2
updated 4 days ago by 41k • written 5 days ago by • 0
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1
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74
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 4 days ago by 41k • written 5 days ago by • 0
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1
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86
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 4 days ago by 41k • written 5 days ago by • 0
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1
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100
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covariate with negative and positive values
DESeq2
updated 4 days ago by 41k • written 6 days ago by • 0
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1
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107
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 4 days ago by ★ 4.0k • written 5 days ago by • 0
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4
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178
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
5 days ago • updated 3 days ago lonn • 0
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3
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167
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 6 days ago by 41k • written 7 days ago by ▴ 20
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214
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How to retrieve detailed regression results from deseq2
DESeq2
12 days ago • updated 3 days ago Weiqian ▴ 10
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4
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223
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DEG with low counts
DESeq2
updated 3 days ago by 41k • written 8 days ago by • 0
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1
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108
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Deseq2 Rlog transformation
DESeq2
updated 7 days ago by ★ 4.0k • written 9 days ago by • 0
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163
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Design Matrix within group comparison more than two groups
DESeq2
10 days ago • updated 9 days ago hemantcnaik • 0
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115
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Bioinformatics student
Des DESeq2
updated 10 days ago by • 0 • written 10 days ago by • 0
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152
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DESeq2 gives an error and R crashes
DESeq2
12 days ago • updated 11 days ago Shefali • 0
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2
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190
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 13 days ago by 41k • written 17 days ago by ▴ 30
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1
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134
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 13 days ago by 41k • written 13 days ago by • 0
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2
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218
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Regressing out batch effects
DESeq2
updated 13 days ago by 41k • written 18 days ago by • 0
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2
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140
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 17 days ago by 65k • written 17 days ago by • 0
1
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1
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152
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DESeq2 - Missing values in count matrix
DESeq2
updated 18 days ago by 65k • written 18 days ago by • 0
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6
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400
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 19 days ago by 41k • written 19 days ago by • 0
1
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1
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133
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
20 days ago Layal • 0
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2
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148
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
20 days ago michelafrancesconi8 • 0
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4
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228
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 20 days ago by 41k • written 21 days ago by • 0
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1
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139
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 25 days ago by 41k • written 25 days ago by • 0
2
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3
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320
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PCA of different bacterial species
DESeq2
updated 26 days ago by 41k • written 27 days ago by ▴ 10
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156
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collapseReplicates dimension error
DESeq2 Dese
updated 28 days ago by 41k • written 4 weeks ago by • 0
3
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2
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196
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
28 days ago Anita ▴ 10
1
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211
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
4 weeks ago • updated 26 days ago Chanderkant Chaudhary • 0
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2
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210
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
4 weeks ago kcarey • 0
2
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3
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281
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DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 4 weeks ago by 41k • written 5 weeks ago by ▴ 20
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3
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239
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Help with Complex DESeq2 Design
DESeq2
updated 4 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
1
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1
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163
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Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2 ctsGE
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
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1
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132
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Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
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1
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163
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lfcShrink error: the line search routine failed
apeglm DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
2
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2
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205
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With DESeq2 "Not full rank" Error with design
DESeq2 DEs
5 weeks ago feather-W • 0
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2
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298
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
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4
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405
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DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
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7
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405
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DESeq2 filtering vs edgeR filtering
DESeq2
5 weeks ago • updated 27 days ago fr8712ca-s • 0
0
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2
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233
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
5 weeks ago kcarey • 0
1
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1
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204
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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
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232
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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
1
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1
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195
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Perform PCA for sample clustering using DESeq2
DESeq2
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
0
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3
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356
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 weeks ago by • 0
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2
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320
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DESeq2: Comparing A Knockout to a Strain
DESeq2
6 weeks ago Viktor Thiel • 0
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1
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201
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DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2 scCITE-seq
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
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8
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372
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
6 weeks ago michelafrancesconi8 • 0
0
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1
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203
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Unusually large fold-changes in Deseq2 results
DESeq2
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
1
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4
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289
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DESeq2 Replicates
DESeq2 RNASeq
6 weeks ago kcarey • 0
2
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6
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322
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Factor vs Character in design
DESeq2
6 weeks ago James Aiden • 0
1
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3
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306
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Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2 glmGamPoi
7 weeks ago • updated 6 weeks ago I-Hsuan Lin ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Methylation Analysis experiment design using Limma by hortense96 • 0
Thank you very much for your reply and your suggestion, as I'm having a bit of trouble finding information on how to manage this part of th…
Comment: Limma design with continuous and categorical covariates by hortense96 • 0
Hello, I'm trying to do a differential methylation analysis with the Limma package and was wondering if you had any suggestions on how to …
Answer: minfi::read.metharray.exp by Basti ▴ 770
Could you show `list.files("~/Users/clarachretienneau/Desktop/clock epigenetic/PJ1209132_ScanData")` ? There may be a problem related to th…
Comment: DESeq2 - dispersion estimation when there is none by WardDeb • 0
Thank you for the pointers, I'll revert back again to the method section of the paper. As for the negative relationship of the estimated di…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by Gayatri • 0
Hello James, How to generate the db? By running the makeOrgPackageFromNCBI() command? I have tried doing that, first by just deleting the …
Votes
Answer: OrgDb for maize
Answer: DESeq2 - dispersion estimation when there is none
Comment: Cannabis and KEGGgraph
Comment: Cannabis and KEGGgraph
Answer: Cannabis and KEGGgraph
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