Showing : edgeR • reset
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How to create design matrix for trait association to modules in WGCNA analysis in R
modules wgcna edgeR limma design
14 hours ago • updated 3 hours ago mohammedtoufiq91 ▴ 10
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1
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90
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DESeq2 or edgeR for Presence and Absence of Proteins
edgeR DESeq2
updated 2 days ago by ★ 2.8k • written 2 days ago by • 0
4
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10
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347
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Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
updated 1 day ago by 47k • written 3 days ago by ▴ 10
5
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7
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246
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Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 3 days ago by 47k • written 4 days ago by ▴ 10
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1
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117
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DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 6 days ago by ★ 1.2k • written 7 days ago by • 0
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1
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125
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CI for logCPM (fitted values)
RNAseq edgeR
updated 10 days ago by 47k • written 10 days ago by ▴ 10
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4
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218
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Anova table edgeR limma
limma RNASeq edgeR
18 days ago • updated 17 days ago KATHERINE CHUERE NUNES • 0
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2
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136
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Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 20 days ago by 47k • written 20 days ago by • 0
1
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3
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214
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Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 25 days ago by 47k • written 27 days ago by • 0
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1
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152
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Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 28 days ago by 47k • written 4 weeks ago by • 0
2
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1
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148
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edgeR with Successive Differences Contrast Coding?
hypothesisTesting contrastCoding edger ExperimentalDesign expressionDifferences
updated 4 weeks ago by 47k • written 4 weeks ago by • 0
0
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3
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216
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edgeR DEGs multilevel
edgeR RNASeq DifferentialRegulation
updated 4 weeks ago by 47k • written 4 weeks ago by • 0
1
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1
reply
193
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Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
DESeq2 edgeR RNAseq
updated 5 weeks ago by 47k • written 5 weeks ago by • 0
1
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1
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140
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Performing a one-sided test for differential expression analysis in edgeR
edgeR
updated 6 weeks ago by ★ 2.8k • written 6 weeks ago by • 0
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88
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Manually adjusting BCV for exactTest in edgeR based on plotBCV
edgeR
6 weeks ago f_rahmdani • 0
0
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1
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150
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Differential express genes in one group across all time points
DESeq2 edgeR BP4RNAseq ensemblVEP
updated 6 weeks ago by 40k • written 6 weeks ago by • 0
2
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2
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200
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How Can I Assess the Reliability of BCV (Square-Root Dispersion) in Non-Replicated Experiments for Differential Expression Analysis Using edgeR?
edgeR
6 weeks ago f_rahmdani • 0
2
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8
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437
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Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
7 weeks ago • updated 1 day ago Luis • 0
0
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1
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157
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Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 7 weeks ago by 47k • written 7 weeks ago by • 0
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1
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113
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Can a expressed gene dataset yielded after CPM be used in DESeq2 and EdgeR?
DESeq2 edgeR
updated 7 weeks ago by ★ 3.6k • written 7 weeks ago by • 0
1
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2
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182
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Performing DE analysis using edgeR for PhIP-seq data with multiple samples, some with some without replicates.
edgeR
8 weeks ago • updated 6 weeks ago f_rahmdani • 0
3
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9
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446
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Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
9 weeks ago • updated 8 weeks ago mohammedtoufiq91 ▴ 10
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2
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260
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
9 weeks ago Giulia • 0
0
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0
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95
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
9 weeks ago Giulia • 0
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0
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148
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Plot profiles for each group - spline analysis in edgeR
timecoursedata edgeR
updated 9 weeks ago by 47k • written 9 weeks ago by ▴ 720
3
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1
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226
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How edgeR estimate the common dispersion?
edgeR
12 weeks ago • updated 9 weeks ago Dan • 0
1
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4
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240
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How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma edgeR RSEM
updated 9 weeks ago by 47k • written 10 weeks ago by ▴ 10
1
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20
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798
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Time-course, comparison of two groups
edgeR
10 weeks ago • updated 7 weeks ago boczniak767 ▴ 720
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99
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Limma: Models containing an intercept and interactions with continuous variables.
limma edgeR DifferentialExpression
10 weeks ago Aashil • 0
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5
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290
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hill-shaped p-value distributions using EdgeR
edgeR p-valuedistribution RNAseq hill-shaped
updated 10 weeks ago by 47k • written 10 weeks ago by • 0
1
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2
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167
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Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2 limma edgeR RSEM
11 weeks ago Yang Shi ▴ 10
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4
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249
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Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
11 weeks ago • updated 10 weeks ago DH • 0
4
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5
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270
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Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 11 weeks ago by ▴ 650 • written 11 weeks ago by ▴ 10
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2
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216
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Is there any reason to think that normalization (e.g. TMM) doesn't work well with samples that that have very different raw counts?
limma RNASeqData edgeR
updated 11 weeks ago by ▴ 30 • written 12 weeks ago by • 0
2
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5
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322
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edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 3 months ago by • 0
0
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3
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265
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Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 3 months ago by 47k • written 3 months ago by • 0
2
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6
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335
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Design matrix for analyzing time points
edgeR
updated 3 months ago by 47k • written 3 months ago by • 0
3
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3
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257
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What is cpmByGroup used for?
edgeR Normalization
updated 3 months ago by 62k • written 3 months ago by • 0
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2
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205
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Using Multi-Dimensional Scaling (MDS) to produce a vector in order to account for patient bias when constructing DGE lists from RNA-seq datasets in R?
PrincipalComponent StatisticalMethod edgeR MultidimensionalScaling Normalization
3 months ago rcreswell01 • 0
2
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8
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502
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Help with inspecting DEs from QLF test and LRT
edgeR
3 months ago Tanner • 0
1
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1
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208
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Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR model.matrix BatchEffect
updated 3 months ago by 62k • written 3 months ago by • 0
6
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11
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556
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Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
3 months ago mohammedtoufiq91 ▴ 10
0
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1
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244
views
Differential expression analysis with global differences among samples (tissues)
DESeq2 qsmooth edgeR limma
updated 3 months ago by 47k • written 3 months ago by • 0
1
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1
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195
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Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 3 months ago by 13k • written 3 months ago by • 0
2
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2
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237
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fomulation of contrasts for blocked design
edgeR
3 months ago chaco001 • 0
3
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5
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450
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Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
3 months ago mohammedtoufiq91 ▴ 10
1
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1
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216
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Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 3 months ago by 47k • written 3 months ago by • 0
2
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1
reply
195
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EdgeR model matrix
edgeR RNASeq
updated 3 months ago by 62k • written 3 months ago by • 0
2
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10
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547
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edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR RNAseq
updated 3 months ago by 47k • written 4 months ago by • 0
3
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5
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405
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Design for DE analysis in tidybulk
DESeq2 designmatrix edgeR limma tidybulk
updated 4 months ago by 40k • written 4 months ago by ▴ 10
50 results • Page 1 of 1
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Comment: BiocGenerics binary is outdated for macOS ARM by jennifer.wokaty ▴ 60
Thanks, Mike, for posting about this and thanks to Lori for noticing the lock. I removed it and RProtoBufLib passes R CMD check. Unfortunat…
Comment: BiocGenerics binary is outdated for macOS ARM by Michael Steinbaugh ▴ 90
Ah thanks for the update. Yeah I see that the flowClust release is the culprit: https://www.bioconductor.org/packages/release/bioc/html/flo…
Comment: Submitting BSgenome package for a new assembly by Manish • 0
Thanks for the info. This is very helpful. -Manish
Comment: Merge 2 accounts, or delete 1 account. by shepherl 3.5k
are you talking specifically on the support site or elsewhere also?
Comment: BiocGenerics binary is outdated for macOS ARM by shepherl 3.5k
That is because it is failing from dependencies not being available. https://bioconductor.org/checkResults/3.17/bioc-mac-arm64-LATEST/BiocG…
Votes
flowCore: using read.FCS with which.lines is not time efficient?
Comment: BiocGenerics binary is outdated for macOS ARM
Comment: Submitting BSgenome package for a new assembly
How to create "trait data" file for WGCNA
Comment: Visualization of negative log CPM values
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