Showing : edgeR • reset
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Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 2 days ago by ★ 4.8k • written 2 days ago by • 0
5
votes
3
replies
752
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 8 days ago by 52k • written 9 days ago by ▴ 10
2
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2
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1.1k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
16 days ago • updated 11 days ago Elizabeth • 0
0
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2
replies
413
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 10 days ago by 43k • written 19 days ago by ▴ 20
0
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1
reply
209
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Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 23 days ago by 52k • written 23 days ago by • 0
0
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4
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1.1k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 23 days ago by • 0 • written 28 days ago by • 0
2
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4
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566
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EdgeR Biological CVs
edgeR
written 9 weeks ago by • 0
3
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5
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1.2k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 10 weeks ago by 68k • written 10 weeks ago by ▴ 10
0
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2
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349
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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
reply
419
views
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
1
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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
vote
9
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979
views
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
votes
10
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2.8k
views
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 4 months ago by ▴ 10
7
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6
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1.0k
views
ANOVA like approach of edgeR
edgeR
updated 4 months ago by 52k • written 4 months ago by ▴ 10
3
votes
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
2
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4
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1.9k
views
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
votes
1
reply
613
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 4 months ago by 68k • written 4 months ago by • 0
3
votes
3
replies
1.1k
views
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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773
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
5 months ago Philippine • 0
4
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6
replies
1.4k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
5 months ago altintas.ali • 0
1
vote
2
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437
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
5 months ago Hongjian • 0
3
votes
3
replies
440
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
5 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
454
views
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
353
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 5 months ago by ★ 4.8k • written 5 months ago by • 0
1
vote
2
replies
609
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 6 months ago by 43k • written 6 months ago by ▴ 10
0
votes
2
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515
views
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
vote
2
replies
439
views
Inconsistent result in edgeR
edgeR
6 months ago hiroko.ohmiya • 0
1
vote
1
reply
581
views
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
votes
9
replies
1.0k
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 7 months ago by 52k • written 7 months ago by • 0
0
votes
3
replies
702
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 7 months ago by • 0
1
vote
1
reply
1.3k
views
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
reply
486
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 7 months ago by 52k • written 7 months ago by • 0
3
votes
3
replies
711
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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
0
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4
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746
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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
views
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
votes
5
replies
2.4k
views
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
votes
4
replies
775
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
9 months ago vohara4 • 0
3
votes
6
replies
996
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
9 months ago JG13 • 0
3
votes
2
replies
840
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
10 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
885
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
vote
3
replies
794
views
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
votes
1
reply
471
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 10 months ago by 52k • written 10 months ago by • 0
4
votes
2
replies
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
vote
2
replies
1.1k
views
Citation for edgeR user guide
edgeR
written 11 months ago by ▴ 30
4
votes
6
replies
1.3k
views
FilterByExpr low counts with small sample size
edgeR
11 months ago Jonathan ▴ 10
0
votes
2
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475
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
11 months ago prity6459 • 0
0
votes
3
replies
723
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 11 months ago by 52k • written 11 months ago by • 0
5
votes
3
replies
1.2k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 10 months ago by 52k • written 11 months ago by • 0
3
votes
3
replies
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: Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files by Mike Smith ★ 6.6k
Tricky to try and debug this without some example files to work with. Can you provide the output of `traceback()` called immediately after…
Answer: Mismatch between Illumina Mouse Methylation BeadChip annotation and genome brows by James W. MacDonald 68k
The annotation data that is provided for this array is simply a repackaging of data that we get from Illumina, so any apparent inconsistenc…
Answer: Package developing and interoperation with Bioconductor by James W. MacDonald 68k
Ideally you would have S4 methods that dispatch on the incoming data structure, so people could call your main function using a `data.frame…
Comment: ComBat with repeated measures by ATpoint ★ 4.8k
It looks to me that you do not need the batch information since subject is nested with batch so correcting for subject will do a paired ana…
Comment: Surprising behavior for DEXseq dispersion estimate plot? by ATpoint ★ 4.8k
You realize this is a spam bot talking to you?
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Answer: Package developing and interoperation with Bioconductor
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
Answer: Explannation for ROAST results
A: How DiffBind run PCA based on peak data?
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
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