Showing : edger • reset
1
vote
2
replies
424
views
Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment edgeR miloR Bioconductor
updated 28 days ago by ★ 4.0k • written 9 weeks ago by • 0
0
votes
1
reply
204
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 8 weeks ago by 53k • written 9 weeks ago by • 0
2
votes
2
replies
287
views
replace cat with message in glmTreat when lfc = 0
edgeR glmTreat
updated 11 weeks ago by 53k • written 11 weeks ago by • 0
0
votes
4
replies
422
views
voomLmFit fitted log-CPM values
limma edgeR
updated 3 months ago by 53k • written 3 months ago by ▴ 10
2
votes
9
replies
957
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
3 months ago mohammedtoufiq91 ▴ 10
3
votes
2
replies
888
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
4 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
935
views
Using offset in edgeR
edgeR
updated 4 months ago by 53k • written 4 months ago by • 0
4
votes
8
replies
1.9k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
4 months ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
replies
5.6k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
4 months ago bbao ▴ 10
5
votes
11
replies
3.2k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 7 months ago by ▴ 10
2
votes
4
replies
2.6k
views
Altered (negative or positive) logFC values for same gene from two intitial count matrices, one being a subset of the other
Transcriptomics edgeR DEG
6 months ago Maziya • 0
2
votes
3
replies
1.5k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
6 months ago Paulito • 0
0
votes
2
replies
879
views
edgeR in DMR mode - replicates give batch effect - how to build design matrix with condition and replicate
edgeR
updated 6 months ago by ▴ 110 • written 6 months ago by • 0
0
votes
3
replies
988
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 8 months ago by ▴ 10
10
votes
13
replies
2.7k
views
edgeR::cpm() results in negative values from raw counts of 0
edgeR
updated 7 months ago by 53k • written 7 months ago by ▴ 20
2
votes
2
replies
1.5k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
5
votes
3
replies
1.2k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 8 months ago by 53k • written 8 months ago by ▴ 10
2
votes
2
replies
1.6k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
9 months ago • updated 8 months ago Elizabeth • 0
0
votes
2
replies
740
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 8 months ago by 43k • written 9 months ago by ▴ 20
0
votes
1
reply
445
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 9 months ago by 53k • written 9 months ago by • 0
0
votes
4
replies
1.4k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 9 months ago by • 0 • written 9 months ago by • 0
2
votes
4
replies
912
views
EdgeR Biological CVs
edgeR
written 10 months ago by • 0
3
votes
5
replies
2.1k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 10 months ago by 68k • written 10 months ago by ▴ 10
0
votes
2
replies
710
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
11 months ago gingergeiger22 • 0
0
votes
1
reply
600
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
1
vote
8
replies
1.6k
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
11 months ago Andre • 0
1
vote
9
replies
1.5k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 11 months ago by ▴ 40
6
votes
10
replies
3.4k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 12 months ago by ★ 5.0k • written 12 months ago by ▴ 10
7
votes
6
replies
1.4k
views
ANOVA like approach of edgeR
edgeR
updated 12 months ago by 53k • written 12 months ago by ▴ 10
3
votes
3
replies
936
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 12 months ago by 53k • written 12 months ago by • 0
2
votes
4
replies
2.5k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 13 months ago by 53k • written 13 months ago by • 0
1
vote
8
replies
2.5k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 13 months ago by • 0
0
votes
1
reply
898
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 13 months ago by 68k • written 13 months ago by • 0
3
votes
3
replies
1.5k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 13 months ago by • 0
0
votes
4
replies
1.1k
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
13 months ago Philippine • 0
4
votes
6
replies
1.8k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
13 months ago altintas.ali • 0
1
vote
2
replies
728
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
13 months ago Hongjian • 0
3
votes
3
replies
762
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
14 months ago • updated 13 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
675
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 14 months ago by 53k • written 14 months ago by • 0
1
vote
1
reply
696
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
1
vote
2
replies
894
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 14 months ago by 43k • written 14 months ago by ▴ 10
0
votes
2
replies
807
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 14 months ago by 53k • written 14 months ago by • 0
1
vote
2
replies
702
views
Inconsistent result in edgeR
edgeR
14 months ago hiroko.ohmiya • 0
1
vote
1
reply
866
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 15 months ago by 53k • written 15 months ago by • 0
2
votes
9
replies
1.5k
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 15 months ago by 53k • written 15 months ago by • 0
0
votes
3
replies
1.0k
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 16 months ago by • 0
2
votes
1
reply
2.2k
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 16 months ago by ★ 29k • written 16 months ago by • 0
0
votes
1
reply
781
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 16 months ago by 53k • written 16 months ago by • 0
3
votes
3
replies
1.1k
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 16 months ago by 68k • written 16 months ago by ▴ 60
0
votes
4
replies
1.1k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 17 months ago by • 0
2,031 results • Page 1 of 41
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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