Showing : DESeq2 • reset
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rlog transformation
DESeq2
updated 1 day ago by 41k • written 2 days ago by • 0
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56
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 1 day ago by 41k • written 2 days ago by • 0
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 1 day ago by 41k • written 3 days ago by • 0
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82
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covariate with negative and positive values
DESeq2
updated 1 day ago by 41k • written 3 days ago by • 0
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84
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 2 days ago by ★ 4.0k • written 3 days ago by • 0
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4
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
3 days ago • updated 8 hours ago lonn • 0
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3
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151
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 4 days ago by 41k • written 5 days ago by ▴ 20
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199
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How to retrieve detailed regression results from deseq2
DESeq2
9 days ago • updated 20 hours ago Weiqian ▴ 10
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4
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205
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DEG with low counts
DESeq2
updated 1 day ago by 41k • written 5 days ago by • 0
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1
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106
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Deseq2 Rlog transformation
DESeq2
updated 5 days ago by ★ 4.0k • written 6 days ago by • 0
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158
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Design Matrix within group comparison more than two groups
DESeq2
7 days ago hemantcnaik • 0
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112
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Bioinformatics student
Des DESeq2
updated 7 days ago by • 0 • written 8 days ago by • 0
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147
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DESeq2 gives an error and R crashes
DESeq2
9 days ago • updated 8 days ago Shefali • 0
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2
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185
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 10 days ago by 41k • written 15 days ago by ▴ 30
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1
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132
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 10 days ago by 41k • written 10 days ago by • 0
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216
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Regressing out batch effects
DESeq2
updated 10 days ago by 41k • written 15 days ago by • 0
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2
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135
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 15 days ago by 65k • written 15 days ago by • 0
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149
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DESeq2 - Missing values in count matrix
DESeq2
updated 15 days ago by 65k • written 16 days ago by • 0
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6
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394
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 16 days ago by 41k • written 16 days ago by • 0
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131
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
18 days ago • updated 17 days ago Layal • 0
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2
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145
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
18 days ago • updated 17 days ago michelafrancesconi8 • 0
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4
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220
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 17 days ago by 41k • written 18 days ago by • 0
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137
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 22 days ago by 41k • written 22 days ago by • 0
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3
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317
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PCA of different bacterial species
DESeq2
updated 24 days ago by 41k • written 24 days ago by ▴ 10
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150
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collapseReplicates dimension error
DESeq2 Dese
updated 25 days ago by 41k • written 29 days ago by • 0
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2
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191
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
26 days ago Anita ▴ 10
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202
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
29 days ago • updated 23 days ago Chanderkant Chaudhary • 0
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204
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
4 weeks ago • updated 29 days ago kcarey • 0
2
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3
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278
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DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 4 weeks ago by 41k • written 4 weeks ago by ▴ 20
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3
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233
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Help with Complex DESeq2 Design
DESeq2
updated 4 weeks ago by ★ 4.0k • written 4 weeks ago by • 0
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160
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Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2 ctsGE
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
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130
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Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
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162
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lfcShrink error: the line search routine failed
apeglm DESeq2
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
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2
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203
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With DESeq2 "Not full rank" Error with design
DESeq2 DEs
5 weeks ago • updated 4 weeks ago feather-W • 0
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294
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
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4
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401
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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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402
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DESeq2 filtering vs edgeR filtering
DESeq2
5 weeks ago • updated 24 days ago fr8712ca-s • 0
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2
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231
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
5 weeks ago kcarey • 0
1
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1
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202
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i'm not getting any differentially expressed genes.
DESeq2
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
2
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225
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Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
1
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194
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Perform PCA for sample clustering using DESeq2
DESeq2
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
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3
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355
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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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2
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317
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DESeq2: Comparing A Knockout to a Strain
DESeq2
6 weeks ago Viktor Thiel • 0
0
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198
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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
0
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8
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370
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
6 weeks ago michelafrancesconi8 • 0
0
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1
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199
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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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288
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DESeq2 Replicates
DESeq2 RNASeq
6 weeks ago kcarey • 0
2
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6
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318
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Factor vs Character in design
DESeq2
6 weeks ago James Aiden • 0
1
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3
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303
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Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2 glmGamPoi
7 weeks ago • updated 6 weeks ago I-Hsuan Lin ▴ 10
4
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7
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833
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weird volcano plot
DESeq2
updated 6 weeks ago by • 0 • written 5 months ago by ▴ 10
50 results • Page 1 of 1
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Thanks Robert!
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Votes
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
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