Showing : DeSeq2 • reset
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DESeq2 v1.35.0
DESeq2
updated 2 hours ago by 41k • written 3 hours ago by • 0
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Deseq2 and Normalization of RNA sequencing data
DESeq2
updated 9 hours ago by ★ 4.1k • written 20 hours ago by • 0
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3
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 8 hours ago by ★ 4.1k • written 20 hours ago by • 0
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93
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Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 22 hours ago by ★ 4.1k • written 23 hours ago by • 0
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 22 hours ago by 41k • written 1 day ago by • 0
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
updated 2 days ago by 41k • written 2 days ago by • 0
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85
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
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putting my own expression data in deseq2
DESeq2
updated 2 days ago by ★ 4.1k • written 2 days ago by • 0
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 3 days ago by ★ 4.1k • written 3 days ago by ▴ 10
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PCA plot suggestions
DESeq2 PCAtools
updated 6 days ago by 41k • written 7 days ago by • 0
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186
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 6 days ago by 41k • written 6 days ago by • 0
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 6 days ago by 65k • written 7 days ago by • 0
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 7 days ago by 41k • written 8 days ago by • 0
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201
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Different Shrunk Log2FC according with reference
DESeq2
updated 8 days ago by 41k • written 8 days ago by ▴ 20
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299
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
8 days ago • updated 6 days ago winwater0928 • 0
3
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295
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 8 days ago by 41k • written 9 days ago by ▴ 40
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8
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 7 days ago by ★ 1.3k • written 9 days ago by • 0
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213
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 9 days ago by 41k • written 10 days ago by • 0
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122
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rlog transformation
DESeq2
updated 14 days ago by 41k • written 14 days ago by • 0
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104
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 14 days ago by 41k • written 14 days ago by • 0
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694
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
15 days ago • updated 6 days ago ussarizona ▴ 10
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128
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covariate with negative and positive values
DESeq2
updated 14 days ago by 41k • written 15 days ago by • 0
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138
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 14 days ago by ★ 4.1k • written 15 days ago by • 0
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229
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
15 days ago • updated 12 days ago lonn • 0
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3
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200
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 16 days ago by 41k • written 17 days ago by ▴ 20
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237
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How to retrieve detailed regression results from deseq2
DESeq2
21 days ago • updated 13 days ago Weiqian ▴ 10
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260
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DEG with low counts
DESeq2
updated 13 days ago by 41k • written 17 days ago by • 0
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127
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Deseq2 Rlog transformation
DESeq2
updated 17 days ago by ★ 4.1k • written 18 days ago by • 0
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2
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188
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Design Matrix within group comparison more than two groups
DESeq2
20 days ago • updated 19 days ago hemantcnaik • 0
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130
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Bioinformatics student
Des DESeq2
updated 20 days ago by • 0 • written 20 days ago by • 0
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173
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DESeq2 gives an error and R crashes
DESeq2
21 days ago • updated 20 days ago Shefali • 0
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214
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 22 days ago by 41k • written 27 days ago by ▴ 30
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157
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 22 days ago by 41k • written 23 days ago by • 0
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233
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Regressing out batch effects
DESeq2
updated 22 days ago by 41k • written 28 days ago by • 0
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159
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 27 days ago by 65k • written 27 days ago by • 0
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160
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DESeq2 - Missing values in count matrix
DESeq2
updated 28 days ago by 65k • written 28 days ago by • 0
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6
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419
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 28 days ago by 41k • written 29 days ago by • 0
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148
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago • updated 29 days ago Layal • 0
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166
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
4 weeks ago • updated 29 days ago michelafrancesconi8 • 0
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4
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452
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DEseq2 coefficient
DESeq2 coefficient
9 weeks ago • updated 1 day ago JKim • 0
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DESeq filtering specific to contrasts
DESeq2
updated 13 days ago by 41k • written 10 weeks ago by • 0
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4
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591
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 16 days ago by 41k • written 6 months ago by • 0
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 15 days ago by • 0 • written 10 months ago by • 0
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19
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2.4k
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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 • 0 • written 4.6 years ago by ▴ 10
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5
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734
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DESeq2 setting significant p-value
DESeq2
updated 13 days ago by 41k • written 5.0 years ago by ▴ 10
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 14 days ago by • 0 • written 8.8 years ago by ▴ 30
47 results • Page 1 of 1
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Answer: DESeq2 v1.35.0 by Michael Love 41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i by James W. MacDonald 65k
Please don't piggyback on posts from 2.3 years ago. If you have a question, post as a new question.
Answer: DESeq2 v1.35.0 by James W. MacDonald 65k
Odd release versions indicate a devel version, which upon release is incremented to the next even version, so you won't be able to find tha…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i by fatinataly • 0
I tried also with oligo does not work, any other suggestion?
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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