Showing : DESEq2 • reset
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
31 minutes ago piemmea • 0
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84
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 3 days ago by ★ 4.1k • written 3 days ago by • 0
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73
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 4 days ago by ★ 4.1k • written 4 days ago by • 0
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7
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294
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
5 days ago • updated 2 days ago sajadahmad41454 • 0
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1
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159
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Handling multiple differential expression comparisons
DESeq2
updated 8 days ago by 42k • written 9 days ago by ▴ 10
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6
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257
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 9 days ago by ★ 1.4k • written 10 days ago by ▴ 130
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3
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222
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 8 days ago by ★ 4.1k • written 9 days ago by • 0
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2
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140
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DESeq2 v1.35.0
DESeq2
updated 11 days ago by 42k • written 11 days ago by • 0
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2
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187
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Deseq2 and Normalization of RNA sequencing data
DESeq2
11 days ago • updated 10 days ago kcarey • 0
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3
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194
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 11 days ago by ★ 4.1k • written 11 days ago by • 0
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3
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278
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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 5 days ago by ★ 4.1k • written 11 days ago by • 0
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3
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283
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 11 days ago by 42k • written 12 days ago by • 0
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1
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140
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 13 days ago by 42k • written 13 days ago by • 0
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2
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150
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
13 days ago • updated 10 days ago Aurora • 0
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126
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 13 days ago by 42k • written 13 days ago by • 0
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126
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putting my own expression data in deseq2
DESeq2
updated 13 days ago by ★ 4.1k • written 13 days ago by • 0
3
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3
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255
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 14 days ago by ★ 4.1k • written 14 days ago by ▴ 10
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2
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220
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PCA plot suggestions
DESeq2 PCAtools
updated 17 days ago by 42k • written 18 days ago by • 0
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3
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240
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 17 days ago by 42k • written 17 days ago by • 0
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9
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408
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 17 days ago by 65k • written 18 days ago by • 0
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162
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 18 days ago by 42k • written 18 days ago by • 0
1
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3
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226
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Different Shrunk Log2FC according with reference
DESeq2
updated 19 days ago by 42k • written 19 days ago by ▴ 20
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4
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347
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
19 days ago • updated 17 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 19 days ago by 42k • written 19 days ago by ▴ 40
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8
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366
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 18 days ago by ★ 1.4k • written 20 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 20 days ago by 42k • written 21 days ago by • 0
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1
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147
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rlog transformation
DESeq2
updated 25 days ago by 42k • written 25 days ago by • 0
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1
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119
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 25 days ago by 42k • written 25 days ago by • 0
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2
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726
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
26 days ago • updated 17 days ago ussarizona ▴ 10
0
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139
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covariate with negative and positive values
DESeq2
updated 25 days ago by 42k • written 26 days ago by • 0
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1
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157
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 25 days ago by ★ 4.1k • written 26 days ago by • 0
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4
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248
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
26 days ago • updated 23 days ago lonn • 0
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3
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214
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 27 days ago by 42k • written 28 days ago by ▴ 20
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2
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250
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How to retrieve detailed regression results from deseq2
DESeq2
4 weeks ago • updated 23 days ago Weiqian ▴ 10
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4
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281
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DEG with low counts
DESeq2
updated 24 days ago by 42k • written 28 days ago by • 0
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1
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138
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Deseq2 Rlog transformation
DESeq2
updated 28 days ago by ★ 4.1k • written 29 days ago by • 0
1
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2
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207
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Design Matrix within group comparison more than two groups
DESeq2
4 weeks ago hemantcnaik • 0
0
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1
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142
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Bioinformatics student
Des DESeq2
updated 4 weeks ago by • 0 • written 4 weeks ago by • 0
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1
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190
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DESeq2 gives an error and R crashes
DESeq2
4 weeks ago Shefali • 0
0
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2
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233
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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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181
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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
0
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2
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256
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Regressing out batch effects
DESeq2
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
0
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2
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180
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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
1
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1
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180
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DESeq2 - Missing values in count matrix
DESeq2
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
1
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6
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453
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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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166
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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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180
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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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278
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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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171
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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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367
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PCA of different bacterial species
DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by ▴ 10
50 results • Page 1 of 1
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Comment: Problem finding certain variables when importing a public database GSE73103 by Guido Hooiveld ★ 3.9k
FWIW: when I would like to make use of publicly available data, I always use the website to explore which metadata is submitted to GEO (and…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
This is `blockLength=200000`, and providing `seg=seg`? It's alright that it's not identical. In the bootstrapped data, you will now have l…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Thank you, Michael. I used the script shared by you. The genomic distribution of the original and null loci looks like non-stationary. Plea…
Comment: ChAMP installation issue by shepherl 3.9k
Without showing the commands you tried and the full output including error it is impossible to help. Please provide additional information…
Answer: Gene set enrichment analysis by Guido Hooiveld ★ 3.9k
No, that is not possible. The idea of gene set enrichment analysis (GSEA) is that it checks which gene sets (pathways, GO categories) are e…
Votes
A: DEXSeq time course design
using variable in design formula
differential expression for Single-cell RNAseq data using edgeR
Why p value inconsistent when using different number of pathway score?
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
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