Showing : DESeq2 • reset
2
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2
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89
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DESeq2 - dispersion estimation when there is none
DESeq2
20 hours ago • updated 5 hours ago WardDeb • 0
0
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4
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179
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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
1
vote
2
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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
0
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7
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383
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DESeq filtering specific to contrasts
DESeq2
updated 3 days ago by 41k • written 9 weeks ago by • 0
5
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14
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2.2k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 3 days ago by • 0 • written 4.6 years ago by ▴ 10
2
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5
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692
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DESeq2 setting significant p-value
DESeq2
updated 3 days ago by 41k • written 5.0 years ago by ▴ 10
0
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4
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225
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DEG with low counts
DESeq2
updated 4 days ago by 41k • written 8 days ago by • 0
0
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1
reply
78
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rlog transformation
DESeq2
updated 4 days ago by 41k • written 5 days ago by • 0
0
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1
reply
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
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
0
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1
reply
100
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covariate with negative and positive values
DESeq2
updated 4 days ago by 41k • written 6 days ago by • 0
9
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12
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7.8k
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 4 days ago by • 0 • written 8.8 years ago by ▴ 30
0
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1
reply
107
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 5 days ago by ★ 4.0k • written 5 days ago by • 0
2
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5
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1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 6 days ago by • 0 • written 10 months ago by • 0
0
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4
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562
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 6 days ago by 41k • written 6 months ago by • 0
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
0
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1
reply
108
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Deseq2 Rlog transformation
DESeq2
updated 8 days ago by ★ 4.0k • written 9 days ago by • 0
1
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2
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163
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Design Matrix within group comparison more than two groups
DESeq2
10 days ago hemantcnaik • 0
0
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1
reply
115
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Bioinformatics student
Des DESeq2
updated 10 days ago by • 0 • written 10 days ago by • 0
0
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1
reply
152
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DESeq2 gives an error and R crashes
DESeq2
12 days ago • updated 11 days ago Shefali • 0
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 18 days ago by ▴ 30
0
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1
reply
135
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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
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
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
reply
152
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DESeq2 - Missing values in count matrix
DESeq2
updated 18 days ago by 65k • written 18 days ago by • 0
1
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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
0
votes
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
1
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1
reply
133
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
20 days ago Layal • 0
0
votes
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
1
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8
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1.2k
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DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 22 days ago by ★ 13k • written 9 months ago by ▴ 10
0
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1
reply
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
1
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2
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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
2
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3
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320
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PCA of different bacterial species
DESeq2
updated 27 days ago by 41k • written 27 days ago by ▴ 10
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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1
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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
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
votes
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
0
votes
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
4
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7
replies
673
views
DESeq2 unable to handle large count values
DESeq2
updated 4 weeks ago by 41k • written 5 months ago by • 0
1
vote
1
reply
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
0
votes
1
reply
132
views
Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
0
votes
1
reply
163
views
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
1
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3
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366
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DEseq2 coefficient
DESeq2 coefficient
8 weeks ago • updated 5 weeks ago JKim • 0
4
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4
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1.1k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2 Dese DifferentialRegulation differe
updated 5 weeks ago by • 0 • written 12 months ago by ▴ 10
0
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4
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405
views
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
0
votes
2
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233
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
5 weeks ago kcarey • 0
0
votes
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
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
50 results • Page 1 of 1
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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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