Showing : deseq2 • reset
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PCA plot suggestions
DESeq2 PCAtools
updated 1 day ago by 41k • written 3 days ago by • 0
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3
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134
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 1 day ago by 41k • written 2 days ago by • 0
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9
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289
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 2 days ago by 65k • written 2 days ago by • 0
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1
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96
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 3 days ago by 41k • written 3 days ago by • 0
1
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3
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148
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Different Shrunk Log2FC according with reference
DESeq2
updated 3 days ago by 41k • written 4 days ago by ▴ 20
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4
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219
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
4 days ago • updated 2 days ago winwater0928 • 0
3
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1
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244
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 4 days ago by 41k • written 4 days ago by ▴ 40
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8
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272
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 3 days ago by ★ 1.3k • written 4 days ago by • 0
3
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3
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186
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 4 days ago by 41k • written 5 days ago by • 0
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1
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105
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rlog transformation
DESeq2
updated 9 days ago by 41k • written 10 days ago by • 0
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1
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93
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 9 days ago by 41k • written 10 days ago by • 0
1
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2
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454
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
10 days ago • updated 1 day ago ussarizona ▴ 10
0
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1
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117
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covariate with negative and positive values
DESeq2
updated 9 days ago by 41k • written 11 days ago by • 0
0
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1
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124
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 9 days ago by ★ 4.0k • written 10 days ago by • 0
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4
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203
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
10 days ago • updated 8 days ago lonn • 0
0
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3
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180
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 11 days ago by 41k • written 12 days ago by ▴ 20
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225
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How to retrieve detailed regression results from deseq2
DESeq2
17 days ago • updated 8 days ago Weiqian ▴ 10
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4
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236
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DEG with low counts
DESeq2
updated 8 days ago by 41k • written 13 days ago by • 0
0
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1
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115
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Deseq2 Rlog transformation
DESeq2
updated 12 days ago by ★ 4.0k • written 14 days ago by • 0
1
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2
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175
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Design Matrix within group comparison more than two groups
DESeq2
15 days ago • updated 14 days ago hemantcnaik • 0
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1
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121
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Bioinformatics student
Des DESeq2
updated 15 days ago by • 0 • written 15 days ago by • 0
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1
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161
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DESeq2 gives an error and R crashes
DESeq2
17 days ago • updated 16 days ago Shefali • 0
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2
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202
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 18 days ago by 41k • written 22 days ago by ▴ 30
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1
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145
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 18 days ago by 41k • written 18 days ago by • 0
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2
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225
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Regressing out batch effects
DESeq2
updated 18 days ago by 41k • written 23 days ago by • 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 22 days ago by 65k • written 22 days ago by • 0
1
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1
reply
156
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DESeq2 - Missing values in count matrix
DESeq2
updated 23 days ago by 65k • written 23 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 24 days ago by 41k • written 24 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
25 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
25 days ago michelafrancesconi8 • 0
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4
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236
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 25 days ago by 41k • written 26 days ago by • 0
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1
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148
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
2
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3
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336
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PCA of different bacterial species
DESeq2
updated 4 weeks ago by 41k • written 4 weeks ago by ▴ 10
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1
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163
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collapseReplicates dimension error
DESeq2 Dese
updated 4 weeks ago by 41k • written 5 weeks ago by • 0
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203
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
4 weeks ago Anita ▴ 10
1
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221
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
5 weeks ago • updated 4 weeks ago Chanderkant Chaudhary • 0
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216
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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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291
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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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249
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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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169
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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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136
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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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171
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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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213
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With DESeq2 "Not full rank" Error with design
DESeq2 DEs
6 weeks ago feather-W • 0
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2
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309
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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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409
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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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414
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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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248
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
6 weeks ago kcarey • 0
1
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1
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211
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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
reply
238
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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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199
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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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Replies
Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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Popular Question to Leo Lahti ▴ 40
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