Showing : DESeq2 • reset
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DESeq2 v1.35.0
DESeq2
just now Espresso • 0
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Deseq2 and Normalization of RNA sequencing data
DESeq2
updated 6 hours ago by ★ 4.1k • written 17 hours ago by • 0
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3
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80
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 5 hours ago by ★ 4.1k • written 17 hours ago by • 0
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91
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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 19 hours ago by ★ 4.1k • written 19 hours ago by • 0
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3
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209
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 18 hours ago by 41k • written 1 day ago by • 0
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76
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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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73
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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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83
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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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80
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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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2
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180
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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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185
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 6 days ago by 41k • written 6 days ago by • 0
2
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9
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340
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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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129
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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 7 days ago by • 0
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200
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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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4
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298
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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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293
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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 8 days ago by ▴ 40
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8
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321
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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
3
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3
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212
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 9 days ago by 41k • written 9 days ago by • 0
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120
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rlog transformation
DESeq2
updated 14 days ago by 41k • written 14 days ago by • 0
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102
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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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690
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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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127
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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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4
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228
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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 12 days ago Weiqian ▴ 10
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4
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259
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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
19 days ago hemantcnaik • 0
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130
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Bioinformatics student
Des DESeq2
updated 19 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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2
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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 22 days ago by • 0
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2
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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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2
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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
1
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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 28 days ago by • 0
1
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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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2
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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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251
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 29 days ago by 41k • written 4 weeks ago by • 0
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157
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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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345
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PCA of different bacterial species
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by ▴ 10
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168
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collapseReplicates dimension error
DESeq2 Dese
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
3
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2
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210
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
5 weeks ago Anita ▴ 10
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2
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228
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
5 weeks ago Chanderkant Chaudhary • 0
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2
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225
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
6 weeks ago • updated 5 weeks ago kcarey • 0
2
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3
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302
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DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 6 weeks ago by 41k • written 6 weeks ago by ▴ 20
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3
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259
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Help with Complex DESeq2 Design
DESeq2
updated 6 weeks ago by ★ 4.1k • written 6 weeks ago by • 0
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174
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Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2 ctsGE
updated 6 weeks ago by 41k • written 6 weeks ago by • 0
50 results • Page 1 of 1
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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 …
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq by james.zhang20 • 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Answer: Deseq2 and Normalization of RNA sequencing data by ATpoint ★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
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A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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