Showing : DESEQ2 • reset
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 7 hours ago by ★ 4.1k • written 10 hours ago by • 0
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3
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74
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 7 hours ago by 42k • written 1 day ago by • 0
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1
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58
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 1 day ago by 42k • written 2 days ago by • 0
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8
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428
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 21 hours ago by ▴ 30 • written 2 days ago by • 0
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1
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46
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
updated 1 day ago by 42k • written 1 day ago by ▴ 30
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1
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125
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 5 days ago by ★ 4.1k • written 5 days ago by • 0
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87
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 6 days ago by ★ 4.1k • written 6 days ago by • 0
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7
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336
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
7 days ago • updated 4 days ago sajadahmad41454 • 0
1
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1
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176
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Handling multiple differential expression comparisons
DESeq2
updated 10 days ago by 42k • written 12 days ago by ▴ 10
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6
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276
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 11 days ago by ★ 1.4k • written 12 days ago by ▴ 130
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3
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243
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 10 days ago by ★ 4.1k • written 12 days ago by • 0
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2
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156
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DESeq2 v1.35.0
DESeq2
updated 13 days ago by 42k • written 13 days ago by • 0
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2
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201
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Deseq2 and Normalization of RNA sequencing data
DESeq2
13 days ago • updated 12 days ago kcarey • 0
0
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3
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204
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 13 days ago by ★ 4.1k • written 13 days ago by • 0
1
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3
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293
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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 7 days ago by ★ 4.1k • written 13 days ago by • 0
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3
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293
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 13 days ago by 42k • written 14 days ago by • 0
1
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1
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146
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 15 days ago by 42k • written 15 days ago by • 0
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2
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161
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
15 days ago • updated 12 days ago Aurora • 0
0
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1
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135
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 15 days ago by 42k • written 15 days ago by • 0
0
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1
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131
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putting my own expression data in deseq2
DESeq2
updated 15 days ago by ★ 4.1k • written 15 days ago by • 0
3
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3
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259
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 16 days ago by ★ 4.1k • written 16 days ago by ▴ 10
0
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2
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224
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PCA plot suggestions
DESeq2 PCAtools
updated 19 days ago by 42k • written 20 days ago by • 0
1
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3
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248
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 19 days ago by 42k • written 19 days ago by • 0
2
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9
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420
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 19 days ago by 65k • written 20 days ago by • 0
0
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1
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164
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 20 days ago by 42k • written 21 days ago by • 0
1
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3
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231
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Different Shrunk Log2FC according with reference
DESeq2
updated 21 days ago by 42k • written 21 days ago by ▴ 20
1
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4
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352
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
21 days ago • updated 19 days ago winwater0928 • 0
3
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1
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325
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 21 days ago by 42k • written 22 days ago by ▴ 40
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8
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376
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 20 days ago by ★ 1.4k • written 22 days ago by • 0
3
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3
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245
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 22 days ago by 42k • written 23 days ago by • 0
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1
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151
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rlog transformation
DESeq2
updated 27 days ago by 42k • written 27 days ago by • 0
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1
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123
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 27 days ago by 42k • written 27 days ago by • 0
1
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2
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732
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
28 days ago • updated 19 days ago Patadù ▴ 10
0
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1
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143
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covariate with negative and positive values
DESeq2
updated 27 days ago by 42k • written 28 days ago by • 0
0
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1
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162
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 27 days ago by ★ 4.1k • written 28 days ago by • 0
0
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4
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257
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
28 days ago • updated 25 days ago lonn • 0
0
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3
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221
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 29 days ago by 42k • written 4 weeks ago by ▴ 20
1
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2
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257
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How to retrieve detailed regression results from deseq2
DESeq2
4 weeks ago • updated 26 days ago Weiqian ▴ 10
0
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4
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289
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DEG with low counts
DESeq2
updated 26 days ago by 42k • written 4 weeks ago by • 0
0
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1
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143
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Deseq2 Rlog transformation
DESeq2
updated 4 weeks ago by ★ 4.1k • written 4 weeks ago by • 0
1
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2
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209
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Design Matrix within group comparison more than two groups
DESeq2
4 weeks ago hemantcnaik • 0
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1
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146
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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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191
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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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240
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 5 weeks ago by 42k • written 5 weeks ago by ▴ 30
0
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1
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183
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
0
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2
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261
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Regressing out batch effects
DESeq2
updated 5 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
reply
183
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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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454
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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 6 weeks ago by • 0
1
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1
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167
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
6 weeks ago Layal • 0
50 results • Page 1 of 1
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Replies
Comment: Create protein sequences including variants from a VCF file by Yun • 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization? by Daniel • 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Guido Hooiveld ★ 4.0k
FWIW: based on [previous posts][1] it is suggested to install like this: install.packages(pkgs="./org.Vdahliae.eg.db", repos=NULL, typ…
Votes
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
Answer: How to design DEXSeq formula for multiple variables
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