Showing : DEseq2 • reset
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 1 hour ago by ▴ 10 • written 17 hours ago by • 0
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4
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168
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
2 days ago • updated 6 hours ago winwater0928 • 0
2
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9
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259
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 17 hours ago by 65k • written 1 day ago by • 0
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1
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65
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PCA plot suggestions
DESeq2 PCAtools
updated 22 hours ago by • 0 • written 1 day ago by • 0
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8
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237
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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
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1
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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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105
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Different Shrunk Log2FC according with reference
DESeq2
updated 2 days ago by 41k • written 2 days ago by ▴ 20
3
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1
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215
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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
6
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16
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2.3k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 days ago by 41k • written 4.6 years ago by ▴ 10
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3
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172
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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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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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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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7
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389
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DESeq filtering specific to contrasts
DESeq2
updated 6 days ago by 41k • written 10 weeks ago by • 0
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5
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700
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DESeq2 setting significant p-value
DESeq2
updated 6 days ago by 41k • written 5.0 years ago by ▴ 10
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4
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230
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DEG with low counts
DESeq2
updated 7 days ago by 41k • written 11 days ago by • 0
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1
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92
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rlog transformation
DESeq2
updated 7 days ago by 41k • written 8 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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1
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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
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
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 7 days ago by • 0 • written 8.8 years ago by ▴ 30
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1
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120
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 8 days ago by ★ 4.0k • written 9 days ago by • 0
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5
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1.1k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 9 days ago by • 0 • written 10 months ago by • 0
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4
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573
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 9 days ago by 41k • written 6 months ago by • 0
0
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3
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176
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 9 days ago by 41k • written 10 days ago by ▴ 20
0
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1
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112
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Deseq2 Rlog transformation
DESeq2
updated 11 days ago by ★ 4.0k • written 12 days ago by • 0
1
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2
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171
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Design Matrix within group comparison more than two groups
DESeq2
13 days ago hemantcnaik • 0
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1
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119
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Bioinformatics student
Des DESeq2
updated 13 days ago by • 0 • written 13 days ago by • 0
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1
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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 21 days ago by ▴ 30
0
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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
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
0
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2
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148
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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
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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
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
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
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 25 days ago by ★ 13k • written 10 months ago by ▴ 10
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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
1
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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
40 results • Page 1 of 1
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Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
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.
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
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?
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