Showing : edgeR • reset
0
votes
1
reply
69
views
segfault in edgeR glmQLFit
edgeR
updated 16 hours ago by 53k • written 1 day ago by • 0
1
vote
2
replies
450
views
Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment edgeR miloR Bioconductor
updated 6 weeks ago by ★ 4.0k • written 11 weeks ago by • 0
0
votes
1
reply
225
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 10 weeks ago by 53k • written 11 weeks ago by • 0
2
votes
2
replies
303
views
replace cat with message in glmTreat when lfc = 0
edgeR glmTreat
updated 3 months ago by 53k • written 3 months ago by • 0
0
votes
4
replies
442
views
voomLmFit fitted log-CPM values
limma edgeR
updated 3 months ago by 53k • written 3 months ago by ▴ 10
2
votes
9
replies
1.0k
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
4 months ago mohammedtoufiq91 ▴ 10
3
votes
2
replies
924
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
5 months ago • updated 4 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
950
views
Using offset in edgeR
edgeR
updated 5 months ago by 53k • written 5 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
5 months ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
replies
5.7k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
5 months ago bbao ▴ 10
5
votes
11
replies
3.3k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 7 months ago by ▴ 10
2
votes
4
replies
2.7k
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
7 months ago • updated 6 months ago Paulito • 0
0
votes
2
replies
896
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 7 months ago by • 0
0
votes
3
replies
1.0k
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 8 months ago by ▴ 10
10
votes
13
replies
2.8k
views
edgeR::cpm() results in negative values from raw counts of 0
edgeR
updated 8 months ago by 53k • written 8 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 9 months ago by ★ 5.0k • written 9 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 9 months ago by 53k • written 9 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 Elizabeth • 0
0
votes
2
replies
764
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 9 months ago by 43k • written 9 months ago by ▴ 20
0
votes
1
reply
458
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
942
views
EdgeR Biological CVs
edgeR
written 11 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 11 months ago by 68k • written 11 months ago by ▴ 10
0
votes
2
replies
732
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
11 months ago gingergeiger22 • 0
0
votes
1
reply
613
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 12 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
1.6k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 12 months ago by ▴ 40
6
votes
10
replies
3.5k
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 13 months ago by ▴ 10
3
votes
3
replies
964
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 13 months ago by 53k • written 13 months ago by • 0
2
votes
4
replies
2.6k
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
2.6k
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
913
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 14 months ago by • 0
0
votes
4
replies
1.1k
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
14 months ago • updated 13 months ago Philippine • 0
4
votes
6
replies
1.9k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
14 months ago altintas.ali • 0
1
vote
2
replies
746
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
14 months ago Hongjian • 0
3
votes
3
replies
781
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
14 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
686
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
715
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
913
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 14 months ago by 43k • written 15 months ago by ▴ 10
0
votes
2
replies
822
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 14 months ago by 53k • written 15 months ago by • 0
1
vote
2
replies
715
views
Inconsistent result in edgeR
edgeR
15 months ago hiroko.ohmiya • 0
1
vote
1
reply
876
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
1.6k
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 16 months ago by • 0
0
votes
3
replies
1.1k
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
807
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
2,032 results • Page 1 of 41
Recent ...
Replies
Comment: blockwiseModule crashes in the end and doesn't generate modules by gexose2839 • 0
Sounds good. @[time][1] [1]: https://timeduration.github.io
Comment: PFAM formats changed - is it still possible to use this with ISA? by TikTsokaasocissalpc • 0
For mobile gaming enthusiasts, 3 Patti Lucky offers a seamless experience, unlike the frustration Harris faced with incompatible PFAM resul…
Answer: segfault in edgeR glmQLFit by Gordon Smyth 53k
Dear Mark, Thank you for providing a reproducible example. I confirm that I can reproduce the segfault myself on my own computer. The prob…
Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by aqeel • 0
Discover the pinnacle of Brazilian Jiu Jitsu gear at [Dragon][1] GI. [1]: https://dragongi.com/
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
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
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Istvan Albert ▴ 50
Popular Question to Dario Strbenac ★ 1.6k
Scholar to Nikos Ignatiadis ▴ 180
Locations • All
United States, 1 minute ago
The city by the bay, 4 minutes ago
United States, 1 hour ago
WEHI, Melbourne, Australia, 3 hours ago
Türkiye, 4 hours ago
Traffic: 838 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