Showing : DEseq2 • reset
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 16 hours ago by ★ 4.1k • written 16 hours ago by • 0
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52
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 1 day ago by ★ 4.1k • written 1 day ago by • 0
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6
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194
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
updated 1 hour ago by ★ 1.4k • written 2 days ago by • 0
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145
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Handling multiple differential expression comparisons
DESeq2
updated 5 days ago by 42k • written 7 days ago by ▴ 10
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6
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246
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 6 days ago by ★ 1.4k • written 8 days ago by ▴ 130
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3
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207
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 5 days ago by ★ 4.1k • written 7 days ago by • 0
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2
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129
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DESeq2 v1.35.0
DESeq2
updated 8 days ago by 42k • written 8 days ago by • 0
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2
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169
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Deseq2 and Normalization of RNA sequencing data
DESeq2
9 days ago • updated 8 days ago kcarey • 0
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3
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173
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 8 days ago by ★ 4.1k • written 9 days ago by • 0
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3
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262
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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 2 days ago by ★ 4.1k • written 9 days ago by • 0
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3
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269
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 9 days ago by 42k • written 10 days ago by • 0
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134
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 10 days ago by 42k • written 10 days ago by • 0
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2
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146
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
10 days ago • updated 7 days ago Aurora • 0
0
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120
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 10 days ago by 42k • written 11 days ago by • 0
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123
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putting my own expression data in deseq2
DESeq2
updated 10 days ago by ★ 4.1k • written 10 days ago by • 0
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249
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 11 days ago by ★ 4.1k • written 11 days ago by ▴ 10
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2
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216
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PCA plot suggestions
DESeq2 PCAtools
updated 14 days ago by 42k • written 15 days ago by • 0
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3
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236
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 14 days ago by 42k • written 15 days ago by • 0
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9
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406
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 15 days ago by 65k • written 15 days ago by • 0
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159
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 16 days ago by 42k • written 16 days ago by • 0
1
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3
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224
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Different Shrunk Log2FC according with reference
DESeq2
updated 16 days ago by 42k • written 16 days ago by ▴ 20
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4
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344
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
16 days ago • updated 14 days ago winwater0928 • 0
3
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1
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319
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 16 days ago by 42k • written 17 days ago by ▴ 40
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8
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362
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 15 days ago by ★ 1.4k • written 17 days ago by • 0
3
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3
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235
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 17 days ago by 42k • written 18 days ago by • 0
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143
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rlog transformation
DESeq2
updated 22 days ago by 42k • written 22 days ago by • 0
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1
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117
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 22 days ago by 42k • written 22 days ago by • 0
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2
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722
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
23 days ago • updated 14 days ago ussarizona ▴ 10
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137
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covariate with negative and positive values
DESeq2
updated 22 days ago by 42k • written 24 days ago by • 0
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156
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 22 days ago by ★ 4.1k • written 23 days ago by • 0
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4
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246
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
23 days ago • updated 20 days ago lonn • 0
0
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3
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210
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 24 days ago by 42k • written 25 days ago by ▴ 20
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2
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248
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How to retrieve detailed regression results from deseq2
DESeq2
4 weeks ago • updated 21 days ago Weiqian ▴ 10
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4
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279
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DEG with low counts
DESeq2
updated 21 days ago by 42k • written 26 days ago by • 0
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136
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Deseq2 Rlog transformation
DESeq2
updated 25 days ago by ★ 4.1k • written 26 days ago by • 0
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2
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201
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Design Matrix within group comparison more than two groups
DESeq2
28 days ago • updated 27 days ago hemantcnaik • 0
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138
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Bioinformatics student
Des DESeq2
updated 28 days ago by • 0 • written 28 days ago by • 0
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183
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DESeq2 gives an error and R crashes
DESeq2
4 weeks ago • updated 29 days ago Shefali • 0
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2
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230
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 4 weeks ago by 42k • written 5 weeks ago by ▴ 30
0
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1
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174
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
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2
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254
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Regressing out batch effects
DESeq2
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
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2
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178
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
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1
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177
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DESeq2 - Missing values in count matrix
DESeq2
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
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6
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449
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
1
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1
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163
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
5 weeks ago Layal • 0
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2
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176
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
5 weeks ago michelafrancesconi8 • 0
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4
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275
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
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1
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170
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
2
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3
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363
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PCA of different bacterial species
DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by ▴ 10
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178
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collapseReplicates dimension error
DESeq2 Dese
updated 6 weeks ago by 42k • written 7 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
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Comment: deseq2 results by swbarnes2 ★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code? by NATASHA • 0
did you find a solution? I´m having the same problem
Comment: error by NATASHA • 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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