Showing : deseq2 • reset
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PCA plot suggestions
DESeq2 PCAtools
6 hours ago Aaliya • 0
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 13 hours ago by 41k • written 17 hours ago by • 0
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Different Shrunk Log2FC according with reference
DESeq2
updated 21 hours ago by 41k • written 1 day ago by ▴ 20
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80
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
1 day ago • updated 3 hours ago winwater0928 • 0
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161
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 1 day ago by 41k • written 1 day ago by ▴ 40
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 5 hours ago by ★ 1.3k • written 1 day ago by • 0
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152
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 1 day ago by 41k • written 2 days ago by • 0
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88
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rlog transformation
DESeq2
updated 6 days ago by 41k • written 7 days ago by • 0
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86
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 6 days ago by 41k • written 7 days ago by • 0
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4
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194
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
7 days ago • updated 5 days ago lonn • 0
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1
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96
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 6 days ago by 41k • written 7 days ago by • 0
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112
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 6 days ago by ★ 4.0k • written 7 days ago by • 0
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112
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covariate with negative and positive values
DESeq2
updated 6 days ago by 41k • written 8 days ago by • 0
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174
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 8 days ago by 41k • written 9 days ago by ▴ 20
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229
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DEG with low counts
DESeq2
updated 5 days ago by 41k • written 10 days ago by • 0
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109
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Deseq2 Rlog transformation
DESeq2
updated 9 days ago by ★ 4.0k • written 11 days ago by • 0
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163
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Design Matrix within group comparison more than two groups
DESeq2
12 days ago • updated 11 days ago hemantcnaik • 0
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Bioinformatics student
Des DESeq2
updated 12 days ago by • 0 • written 12 days ago by • 0
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155
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DESeq2 gives an error and R crashes
DESeq2
14 days ago • updated 13 days ago Shefali • 0
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217
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How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago Weiqian ▴ 10
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137
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 15 days ago by 41k • written 15 days ago by • 0
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142
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 19 days ago by 65k • written 19 days ago by • 0
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192
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 15 days ago by 41k • written 19 days ago by ▴ 30
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220
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Regressing out batch effects
DESeq2
updated 15 days ago by 41k • written 20 days ago by • 0
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152
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DESeq2 - Missing values in count matrix
DESeq2
updated 20 days ago by 65k • written 20 days ago by • 0
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 21 days ago by 41k • written 21 days ago by • 0
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136
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
22 days ago Layal • 0
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152
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
22 days ago michelafrancesconi8 • 0
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4
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229
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 22 days ago by 41k • written 23 days ago by • 0
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142
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 27 days ago by 41k • written 27 days ago by • 0
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PCA of different bacterial species
DESeq2
updated 28 days ago by 41k • written 29 days ago by ▴ 10
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199
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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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158
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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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212
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
4 weeks ago • updated 28 days ago Chanderkant Chaudhary • 0
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
5 weeks ago • updated 4 weeks ago kcarey • 0
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243
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Help with Complex DESeq2 Design
DESeq2
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
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285
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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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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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164
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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
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1
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164
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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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207
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With DESeq2 "Not full rank" Error with design
DESeq2 DEs
5 weeks ago feather-W • 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 6 weeks ago by • 0
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236
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
6 weeks ago • updated 5 weeks ago kcarey • 0
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406
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DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 29 days ago fr8712ca-s • 0
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302
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 5 weeks ago by 41k • written 6 weeks ago by • 0
2
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233
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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
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206
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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
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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
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2
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321
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DESeq2: Comparing A Knockout to a Strain
DESeq2
6 weeks ago Viktor Thiel • 0
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207
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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
50 results • Page 1 of 1
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Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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