Showing : DESeq2 • reset
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 1 hour ago by ★ 4.0k • written 14 hours ago by • 0
2
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9
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238
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 13 hours ago by 65k • written 21 hours ago by • 0
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PCA plot suggestions
DESeq2 PCAtools
updated 19 hours ago by • 0 • written 1 day ago by • 0
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1
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77
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 1 day ago by 41k • written 1 day ago by • 0
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3
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103
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Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by 41k • written 2 days ago by ▴ 20
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4
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148
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
2 days ago • updated 3 hours ago winwater0928 • 0
3
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1
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214
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 2 days ago by 41k • written 2 days ago by ▴ 40
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8
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 1 day ago by ★ 1.3k • written 2 days ago by • 0
3
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3
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171
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
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91
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rlog transformation
DESeq2
updated 7 days ago by 41k • written 7 days ago by • 0
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1
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90
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 7 days ago by 41k • written 8 days ago by • 0
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99
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 7 days ago by 41k • written 8 days ago by • 0
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1
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115
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covariate with negative and positive values
DESeq2
updated 7 days ago by 41k • written 9 days ago by • 0
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1
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119
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 7 days ago by ★ 4.0k • written 8 days ago by • 0
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4
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199
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
8 days ago • updated 6 days ago lonn • 0
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3
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 9 days ago by 41k • written 10 days ago by ▴ 20
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2
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220
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How to retrieve detailed regression results from deseq2
DESeq2
15 days ago • updated 6 days ago Weiqian ▴ 10
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4
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230
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DEG with low counts
DESeq2
updated 6 days ago by 41k • written 11 days ago by • 0
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1
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112
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Deseq2 Rlog transformation
DESeq2
updated 10 days ago by ★ 4.0k • written 12 days ago by • 0
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2
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169
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Design Matrix within group comparison more than two groups
DESeq2
13 days ago • updated 12 days ago hemantcnaik • 0
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118
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Bioinformatics student
Des DESeq2
updated 13 days ago by • 0 • written 13 days ago by • 0
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159
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DESeq2 gives an error and R crashes
DESeq2
15 days ago • updated 14 days ago Shefali • 0
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2
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197
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 16 days ago by 41k • written 20 days ago by ▴ 30
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1
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143
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 16 days ago by 41k • written 16 days ago by • 0
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2
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225
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Regressing out batch effects
DESeq2
updated 16 days ago by 41k • written 21 days ago by • 0
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2
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147
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 20 days ago by 65k • written 20 days ago by • 0
1
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1
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155
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DESeq2 - Missing values in count matrix
DESeq2
updated 21 days ago by 65k • written 21 days ago by • 0
1
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6
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407
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 22 days ago by 41k • written 22 days ago by • 0
1
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1
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139
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
23 days ago Layal • 0
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2
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154
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
23 days ago michelafrancesconi8 • 0
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4
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234
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 23 days ago by 41k • written 24 days ago by • 0
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1
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144
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 28 days ago by 41k • written 28 days ago by • 0
2
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3
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329
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PCA of different bacterial species
DESeq2
updated 29 days ago by 41k • written 4 weeks ago by ▴ 10
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1
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161
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collapseReplicates dimension error
DESeq2 Dese
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
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2
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202
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
4 weeks ago Anita ▴ 10
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2
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216
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
5 weeks ago • updated 29 days ago Chanderkant Chaudhary • 0
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2
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213
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
5 weeks ago kcarey • 0
2
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3
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287
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DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by ▴ 20
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3
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246
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Help with Complex DESeq2 Design
DESeq2
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
1
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1
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166
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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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134
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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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167
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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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209
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With DESeq2 "Not full rank" Error with design
DESeq2 DEs
6 weeks ago • updated 5 weeks ago feather-W • 0
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2
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305
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 6 weeks ago by 41k • written 6 weeks ago by • 0
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4
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407
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DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 6 weeks ago by 41k • written 6 weeks ago by • 0
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7
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411
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DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 4 weeks ago fr8712ca-s • 0
0
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2
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243
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
6 weeks ago kcarey • 0
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1
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210
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i'm not getting any differentially expressed genes.
DESeq2
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
2
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1
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236
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Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
1
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1
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197
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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
50 results • Page 1 of 1
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Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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