Showing : EDGER • reset
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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 2.7 years ago by 53k • written 2.7 years ago by • 0
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1
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1.2k
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Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
2
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1
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1.1k
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edgeR with Successive Differences Contrast Coding?
hypothesisTesting contrastCoding edger ExperimentalDesign expressionDifferences
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
0
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3
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1.3k
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edgeR DEGs multilevel
edgeR RNASeq DifferentialRegulation
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
1
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1
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750
views
Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
DESeq2 edgeR RNAseq
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
1
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1
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876
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Performing a one-sided test for differential expression analysis in edgeR
edgeR
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
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0
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999
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Manually adjusting BCV for exactTest in edgeR based on plotBCV
edgeR
2.8 years ago f_rahmdani • 0
0
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1
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797
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Differential express genes in one group across all time points
DESeq2 edgeR BP4RNAseq ensemblVEP
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
2
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2
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951
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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
2.8 years ago f_rahmdani • 0
2
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8
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4.5k
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Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
2.8 years ago • updated 2.6 years ago Luis • 0
0
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1
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1.1k
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Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
0
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1
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701
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Can a expressed gene dataset yielded after CPM be used in DESeq2 and EdgeR?
DESeq2 edgeR
updated 2.8 years ago by ★ 4.1k • written 2.8 years ago by • 0
1
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2
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Performing DE analysis using edgeR for PhIP-seq data with multiple samples, some with some without replicates.
edgeR
2.8 years ago f_rahmdani • 0
3
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9
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3.6k
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Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
2.8 years ago mohammedtoufiq91 ▴ 10
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2
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2.2k
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.8 years ago Giulia • 0
0
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0
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855
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.8 years ago Giulia • 0
0
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0
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833
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Plot profiles for each group - spline analysis in edgeR
timecoursedata edgeR
updated 2.8 years ago by 53k • written 2.8 years ago by ▴ 740
3
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1
reply
896
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How edgeR estimate the common dispersion?
edgeR
2.9 years ago • updated 2.8 years ago Dan • 0
1
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4
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2.8k
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How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma edgeR RSEM
updated 2.8 years ago by 53k • written 2.8 years ago by ▴ 10
3
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20
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3.8k
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Time-course, comparison of two groups
edgeR
2.8 years ago boczniak767 ▴ 740
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0
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782
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Limma: Models containing an intercept and interactions with continuous variables.
limma edgeR DifferentialExpression
2.8 years ago Aashil • 0
0
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5
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1.7k
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hill-shaped p-value distributions using EdgeR
edgeR p-valuedistribution RNAseq hill-shaped
updated 2.8 years ago by 53k • written 2.9 years ago by • 0
1
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2
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1.2k
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Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2 limma edgeR RSEM
2.9 years ago Yang Shi ▴ 10
1
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4
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1.4k
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Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
2.9 years ago DH • 0
4
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5
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3.1k
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Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 2.9 years ago by ▴ 760 • written 2.9 years ago by ▴ 10
0
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2
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1.2k
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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 2.9 years ago by ▴ 40 • written 2.9 years ago by • 0
2
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5
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2.8k
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edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 2.9 years ago by • 0
0
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3
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1.5k
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Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
2
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6
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1.3k
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Design matrix for analyzing time points
edgeR
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
3
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3
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1.3k
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What is cpmByGroup used for?
edgeR Normalization
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
0
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2
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1.4k
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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
2.9 years ago rcreswell01 • 0
2
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8
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2.3k
views
Help with inspecting DEs from QLF test and LRT
edgeR
2.9 years ago Tanner • 0
1
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1
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1.4k
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR model.matrix BatchEffect
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
6
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11
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2.5k
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Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
2.9 years ago mohammedtoufiq91 ▴ 10
0
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1
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1.2k
views
Differential expression analysis with global differences among samples (tissues)
DESeq2 qsmooth edgeR limma
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
1
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1
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1.5k
views
Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 2.9 years ago by ★ 13k • written 2.9 years ago by ▴ 70
2
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2
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1.0k
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fomulation of contrasts for blocked design
edgeR
2.9 years ago chaco001 • 0
6
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10
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4.5k
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Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 21 months ago by • 0 • written 3.0 years ago by ▴ 10
1
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1
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1.4k
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Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
2
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1
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798
views
EdgeR model matrix
edgeR RNASeq
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
2
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10
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2.0k
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edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR RNAseq
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
3
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5
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1.8k
views
Design for DE analysis in tidybulk
DESeq2 designmatrix edgeR limma tidybulk
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 10
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1
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1.3k
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Subset count data in DGEList using edgeR/DESeq2
edgeR DMR
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
3
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2
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1.1k
views
Help with the design matrix for longitudinal study
edgeR
3.0 years ago sharvari gujja ▴ 40
1
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3
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1.5k
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Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2 edgeR rnaseqGene
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
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2
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1.3k
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Orange point meaning in plotSmear with edgeR
edgeR plotSmear
3.0 years ago Tess • 0
0
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3
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1.4k
views
Differential gene expression analysis with data matrix generated with RSEM
DESeq2 edgeR
3.0 years ago ubjw24 • 0
1
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1
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1.1k
views
Alternatives to Voom in experiments without replicate
limma edgeR Voom
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
1
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1
reply
1.4k
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Extracting the tophits from limma Volcanoplot and issue with geneIDs
limma edgeR Glimma
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
2
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5
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1.9k
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Create the design matrix
DEGseq edgeR RNASeq
3.1 years ago Mohammad • 0
2,035 results • Page 4 of 41
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Answer: Are individual-mouse-based statistics possible in CellChat? by ATpoint ★ 5.0k
Not a Bioconductor package, I commented on the crosspost at https://www.biostars.org/p/9617271/
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apeglm is more cumbersome than ashr as with apeglm the coefficients need to be explicitely available in the resultsNames.So, you need to re…
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I see rstudioapi in the `sessionInfo()`. RStudio does not support forked ('multicore') processes. Does the BiocParallel example work when y…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
Given that this is an issue with BiocParallel on your machine and we have a minimal reproducible example, you may want to repost the issue.…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Benjamin • 0
Still happening using pre-existing size factors estimating dispersions gene-wise dispersion estimates: 15 workers mean-dis…
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A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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