Showing : EdgeR • reset
1
vote
2
replies
404
views
Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment edgeR miloR Bioconductor
updated 13 days ago by ★ 4.0k • written 7 weeks ago by • 0
0
votes
1
reply
194
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 6 weeks ago by 53k • written 7 weeks ago by • 0
2
votes
2
replies
277
views
replace cat with message in glmTreat when lfc = 0
edgeR glmTreat
updated 9 weeks ago by 53k • written 9 weeks ago by • 0
0
votes
4
replies
410
views
voomLmFit fitted log-CPM values
limma edgeR
updated 10 weeks ago by 53k • written 11 weeks ago by ▴ 10
2
votes
9
replies
940
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
870
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
4 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
924
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 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
1.5k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
6 months ago Paulito • 0
0
votes
2
replies
867
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 6 months ago by • 0
0
votes
3
replies
975
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 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
8 months ago Elizabeth • 0
0
votes
2
replies
731
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 8 months ago by 43k • written 8 months ago by ▴ 20
0
votes
1
reply
437
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
900
views
EdgeR Biological CVs
edgeR
written 10 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 10 months ago by 68k • written 10 months ago by ▴ 10
0
votes
2
replies
700
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
10 months ago gingergeiger22 • 0
0
votes
1
reply
594
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 11 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 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 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 12 months ago by ▴ 10
3
votes
3
replies
911
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 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
889
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 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 • updated 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
13 months ago altintas.ali • 0
1
vote
2
replies
718
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
13 months ago Hongjian • 0
3
votes
3
replies
743
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
13 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
667
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
691
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
879
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 13 months ago by 43k • written 14 months ago by ▴ 10
0
votes
2
replies
790
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 13 months ago by 53k • written 14 months ago by • 0
1
vote
2
replies
694
views
Inconsistent result in edgeR
edgeR
14 months ago hiroko.ohmiya • 0
1
vote
1
reply
857
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 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 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
772
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
1.1k
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: How can I correctly use phyloseq with Docker? by Kevin Blighe ★ 4.0k
The Bioconductor version must be compatible with the R version. Bioconductor version 3.18 is compatible with R version 4.3. The Dockerfile …
Answer: Boolean Gate Combination for Any 2 Positive Events in flowWorkspace by Kevin Blighe ★ 4.0k
Your proposed code is correct and will achieve the desired outcome. The boolean filter expression `IFNg & TNFa | IFNg & IL2 | TNFa & IL2` i…
Answer: Install old version of DESeq2 by Kevin Blighe ★ 4.0k
The Dockerfile that you have provided is appropriate for installing DESeq2 and apeglm from Bioconductor release 3.10, which corresponds to …
Answer: Guidance Requested on GCN Network Analysis and Module Enrichment in R by Kevin Blighe ★ 4.0k
The discrepancy between `final_exp1` and `final_exp2` could arise from several factors, despite matching dimensions. The `identical()` func…
Answer: ORFik: spliced 5utr regions by Kevin Blighe ★ 4.0k
Hello Luna. The findUORFs function in ORFik identifies upstream open reading frames by extracting and concatenating the sequences of exo…
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
Awards • All
Scholar to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Supporter to fabio.marroni • 0
Popular Question to Guido Hooiveld ★ 4.1k
Popular Question to James W. MacDonald 68k
Locations • All
The Cave, 181 Longwood Avenue, Boston, USA, 22 minutes ago
Saudi Arabia, 24 minutes ago
United States, 1 hour ago
United States, 1 hour ago
United States, 2 hours ago
Traffic: 928 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6