Showing : DESeq2 • reset
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 2 hours ago by 41k • written 9 hours ago by ▴ 40
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
12 hours ago • updated 41 minutes ago Aaliya • 0
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135
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 14 hours ago by 41k • written 1 day ago by • 0
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83
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rlog transformation
DESeq2
updated 5 days ago by 41k • written 5 days ago by • 0
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83
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 5 days ago by 41k • written 5 days ago by • 0
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 5 days ago by 41k • written 6 days ago by • 0
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105
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covariate with negative and positive values
DESeq2
updated 5 days ago by 41k • written 7 days ago by • 0
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109
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 5 days ago by ★ 4.0k • written 6 days ago by • 0
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187
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
6 days ago • updated 3 days ago lonn • 0
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168
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 7 days ago by 41k • written 8 days ago by ▴ 20
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215
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How to retrieve detailed regression results from deseq2
DESeq2
13 days ago • updated 4 days ago Weiqian ▴ 10
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227
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DEG with low counts
DESeq2
updated 4 days ago by 41k • written 9 days ago by • 0
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108
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Deseq2 Rlog transformation
DESeq2
updated 8 days ago by ★ 4.0k • written 9 days ago by • 0
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163
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Design Matrix within group comparison more than two groups
DESeq2
11 days ago • updated 10 days ago hemantcnaik • 0
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115
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Bioinformatics student
Des DESeq2
updated 11 days ago by • 0 • written 11 days ago by • 0
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152
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DESeq2 gives an error and R crashes
DESeq2
13 days ago • updated 12 days ago Shefali • 0
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191
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 14 days ago by 41k • written 18 days ago by ▴ 30
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135
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 14 days ago by 41k • written 14 days ago by • 0
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219
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Regressing out batch effects
DESeq2
updated 14 days ago by 41k • written 19 days ago by • 0
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141
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 18 days ago by 65k • written 18 days ago by • 0
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152
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DESeq2 - Missing values in count matrix
DESeq2
updated 19 days ago by 65k • written 19 days ago by • 0
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 20 days ago by 41k • written 20 days ago by • 0
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135
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
21 days ago • updated 20 days ago Layal • 0
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149
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
21 days ago • updated 20 days ago michelafrancesconi8 • 0
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228
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 21 days ago by 41k • written 22 days ago by • 0
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140
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 26 days ago by 41k • written 26 days ago by • 0
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320
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PCA of different bacterial species
DESeq2
updated 27 days ago by 41k • written 28 days ago by ▴ 10
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157
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collapseReplicates dimension error
DESeq2 Dese
updated 29 days ago by 41k • written 4 weeks ago by • 0
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196
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
29 days ago Anita ▴ 10
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211
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
4 weeks ago • updated 27 days ago Chanderkant Chaudhary • 0
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210
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
4 weeks ago kcarey • 0
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282
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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
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240
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Help with Complex DESeq2 Design
DESeq2
updated 4 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
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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
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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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163
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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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206
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With DESeq2 "Not full rank" Error with design
DESeq2 DEs
5 weeks ago feather-W • 0
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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 6 weeks ago by • 0
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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 5 weeks ago by • 0
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406
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DESeq2 filtering vs edgeR filtering
DESeq2
5 weeks ago • updated 28 days ago fr8712ca-s • 0
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234
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
5 weeks ago kcarey • 0
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205
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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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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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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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358
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 weeks ago by • 0
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320
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DESeq2: Comparing A Knockout to a Strain
DESeq2
6 weeks ago Viktor Thiel • 0
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204
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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
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8
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373
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
6 weeks ago michelafrancesconi8 • 0
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203
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Unusually large fold-changes in Deseq2 results
DESeq2
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
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4
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289
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DESeq2 Replicates
DESeq2 RNASeq
6 weeks ago kcarey • 0
50 results • Page 1 of 1
Recent ...
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Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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