Showing : edger • reset
1
vote
2
replies
372
views
Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment edgeR miloR Bioconductor
updated 2 days ago by ★ 4.0k • written 5 weeks ago by • 0
0
votes
1
reply
171
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 4 weeks ago by 53k • written 5 weeks ago by • 0
0
votes
2
replies
251
views
replace cat with message in glmTreat when lfc = 0
edgeR glmTreat
updated 7 weeks ago by 53k • written 8 weeks ago by • 0
0
votes
4
replies
402
views
voomLmFit fitted log-CPM values
limma edgeR
updated 9 weeks ago by 53k • written 9 weeks ago by ▴ 10
2
votes
9
replies
921
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
855
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
3 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
919
views
Using offset in edgeR
edgeR
updated 3 months ago by 53k • written 3 months ago by • 0
4
votes
8
replies
1.8k
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 • updated 3 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 • updated 3 months ago bbao ▴ 10
5
votes
11
replies
3.2k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 6 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
5 months ago Maziya • 0
2
votes
3
replies
1.4k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
5 months ago Paulito • 0
0
votes
2
replies
848
views
edgeR in DMR mode - replicates give batch effect - how to build design matrix with condition and replicate
edgeR
updated 5 months ago by ▴ 110 • written 5 months ago by • 0
0
votes
3
replies
964
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 7 months ago by ▴ 10
10
votes
13
replies
2.6k
views
edgeR::cpm() results in negative values from raw counts of 0
edgeR
updated 6 months ago by 53k • written 6 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 7 months ago by ★ 5.0k • written 7 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 7 months ago by 53k • written 7 months ago by ▴ 10
2
votes
2
replies
1.5k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
8 months ago • updated 7 months ago Elizabeth • 0
0
votes
2
replies
724
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 7 months ago by 43k • written 8 months ago by ▴ 20
0
votes
1
reply
431
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 8 months ago by 53k • written 8 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 8 months ago by • 0 • written 8 months ago by • 0
2
votes
4
replies
888
views
EdgeR Biological CVs
edgeR
written 9 months ago by • 0
3
votes
5
replies
2.0k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 9 months ago by 68k • written 9 months ago by ▴ 10
0
votes
2
replies
689
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
10 months ago gingergeiger22 • 0
0
votes
1
reply
590
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 10 months ago by 43k • written 10 months ago by • 0
1
vote
8
replies
1.6k
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
10 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 10 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 11 months ago by ★ 5.0k • written 11 months ago by ▴ 10
7
votes
6
replies
1.4k
views
ANOVA like approach of edgeR
edgeR
updated 11 months ago by 53k • written 11 months ago by ▴ 10
3
votes
3
replies
904
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 11 months ago by 53k • written 11 months ago by • 0
2
votes
4
replies
2.5k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 12 months ago by 53k • written 12 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 12 months ago by • 0
0
votes
1
reply
879
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 12 months ago by 68k • written 12 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 12 months ago by • 0
0
votes
4
replies
1.1k
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
12 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
12 months ago altintas.ali • 0
1
vote
2
replies
710
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
12 months ago Hongjian • 0
3
votes
3
replies
730
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
13 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
657
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 13 months ago by 53k • written 13 months ago by • 0
1
vote
1
reply
645
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
1
vote
2
replies
864
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 13 months ago by 43k • written 13 months ago by ▴ 10
0
votes
2
replies
780
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 13 months ago by 53k • written 13 months ago by • 0
1
vote
2
replies
684
views
Inconsistent result in edgeR
edgeR
13 months ago hiroko.ohmiya • 0
1
vote
1
reply
848
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 14 months ago by 53k • written 14 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 14 months ago by 53k • written 14 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 15 months ago by • 0
2
votes
1
reply
2.1k
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 15 months ago by ★ 29k • written 15 months ago by • 0
0
votes
1
reply
762
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 15 months ago by 53k • written 15 months ago by • 0
3
votes
3
replies
1.0k
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 15 months ago by 68k • written 15 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 16 months ago by • 0
2,031 results • Page 1 of 41
Recent ...
Replies
Answer: Add additional maintainer for MOFA2 by shepherl 4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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