Showing : edgeR • reset
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Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 6 hours ago by ★ 4.8k • written 21 hours ago by • 0
5
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3
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742
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Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 6 days ago by 52k • written 7 days ago by ▴ 10
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2
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1.1k
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Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
15 days ago • updated 9 days ago Elizabeth • 0
0
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2
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408
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 9 days ago by 43k • written 17 days ago by ▴ 20
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1
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203
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Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 21 days ago by 52k • written 21 days ago by • 0
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4
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1.1k
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DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 21 days ago by • 0 • written 26 days ago by • 0
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4
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562
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EdgeR Biological CVs
edgeR
written 9 weeks ago by • 0
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5
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1.2k
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Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 9 weeks ago by 68k • written 9 weeks ago by ▴ 10
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2
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347
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Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
11 weeks ago gingergeiger22 • 0
0
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1
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414
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Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 11 weeks ago by 43k • written 3 months ago by • 0
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8
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1.0k
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Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
12 weeks ago • updated 11 weeks ago Andre • 0
1
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9
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977
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 3 months ago by ▴ 30
6
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10
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2.8k
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What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 3 months ago by ★ 4.8k • written 3 months ago by ▴ 10
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6
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1.0k
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ANOVA like approach of edgeR
edgeR
updated 3 months ago by 52k • written 4 months ago by ▴ 10
3
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3
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645
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 4 months ago by 52k • written 4 months ago by • 0
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4
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1.9k
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Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 4 months ago by 52k • written 4 months ago by • 0
1
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8
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1.7k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 4 months ago by • 0
0
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1
reply
611
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single cell RNA seq pseudobulk batch correction
edgeR
updated 4 months ago by 68k • written 4 months ago by • 0
3
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3
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1.1k
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 5 months ago by • 0
0
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4
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772
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
5 months ago • updated 4 months ago Philippine • 0
4
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6
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1.4k
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Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
5 months ago altintas.ali • 0
1
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2
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435
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edgeR 4.2.2 not compiled for Windows
edger edgeR
5 months ago Hongjian • 0
3
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3
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439
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How to subset voomLmFit (MArrayLM) object?
limma edgeR
5 months ago Guido Hooiveld ★ 4.1k
4
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1
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452
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edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 5 months ago by 52k • written 5 months ago by • 0
1
vote
1
reply
352
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 5 months ago by ★ 4.8k • written 5 months ago by • 0
1
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2
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608
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 5 months ago by 43k • written 6 months ago by ▴ 10
0
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2
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513
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EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 5 months ago by 52k • written 6 months ago by • 0
1
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2
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439
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Inconsistent result in edgeR
edgeR
6 months ago hiroko.ohmiya • 0
1
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1
reply
580
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Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 6 months ago by 52k • written 6 months ago by • 0
2
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9
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1.0k
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Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 6 months ago by 52k • written 7 months ago by • 0
0
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3
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702
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 7 months ago by • 0
1
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1
reply
1.3k
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 7 months ago by ★ 28k • written 7 months ago by • 0
0
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1
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485
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edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 7 months ago by 52k • written 7 months ago by • 0
3
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3
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709
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Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 7 months ago by 68k • written 7 months ago by ▴ 50
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4
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745
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 8 months ago by • 0
1
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8
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1.3k
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Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 8 months ago by 52k • written 9 months ago by • 0
3
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5
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2.4k
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 9 months ago by • 0 • written 12 months ago by ▴ 60
0
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4
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772
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
9 months ago vohara4 • 0
3
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6
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995
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Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
9 months ago JG13 • 0
3
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2
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839
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
10 months ago mohammedtoufiq91 ▴ 10
3
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3
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883
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 10 months ago by 52k • written 10 months ago by • 0
1
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3
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792
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 10 months ago by 52k • written 10 months ago by • 0
0
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1
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470
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 10 months ago by 52k • written 10 months ago by • 0
4
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2
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1.4k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
10 months ago gene_bioconductor ▴ 10
1
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2
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1.1k
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Citation for edgeR user guide
edgeR
written 11 months ago by ▴ 30
4
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6
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1.3k
views
FilterByExpr low counts with small sample size
edgeR
11 months ago Jonathan ▴ 10
0
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2
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475
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
11 months ago prity6459 • 0
0
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3
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723
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 11 months ago by 52k • written 11 months ago by • 0
5
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3
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1.2k
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Log-cpm values from limma
limma edgeR RNASeq
updated 10 months ago by 52k • written 11 months ago by • 0
3
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3
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1.3k
views
permutation test in edgeR
rna-seq edgeR
updated 11 months ago by 52k • written 11 months ago by • 0
50 results • Page 1 of 1
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Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k
If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Benjamin ▴ 20
I have received a response from Ensembl regarding the items I have listed above. I wanted to post it here and will continue to post update…
Votes
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
A: Is logFC a log2 fold change or some other base in scran::findMarkers
Comment: Error in retrieving clinical data
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