Showing : EDGER • reset
2
votes
9
replies
489
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
21 days ago • updated 19 days ago mohammedtoufiq91 ▴ 10
3
votes
2
replies
734
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
5 weeks ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
829
views
Using offset in edgeR
edgeR
updated 6 weeks ago by 52k • written 6 weeks ago by • 0
4
votes
8
replies
1.7k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
7 weeks ago • updated 6 weeks ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
replies
5.3k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
7 weeks ago • updated 6 weeks ago bbao ▴ 10
5
votes
11
replies
2.9k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 4 months ago by ▴ 10
2
votes
4
replies
2.5k
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
3 months ago Maziya • 0
2
votes
3
replies
1.2k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
3 months ago Paulito • 0
0
votes
2
replies
772
views
edgeR in DMR mode - replicates give batch effect - how to build design matrix with condition and replicate
edgeR
updated 3 months ago by ▴ 110 • written 3 months ago by • 0
0
votes
3
replies
872
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 4 months ago by ▴ 10
10
votes
13
replies
2.2k
views
edgeR::cpm() results in negative values from raw counts of 0
edgeR
updated 4 months ago by 52k • written 4 months ago by ▴ 20
2
votes
2
replies
1.4k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 5 months ago by ★ 4.9k • written 5 months ago by • 0
5
votes
3
replies
1.1k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 5 months ago by 52k • written 5 months ago by ▴ 10
2
votes
2
replies
1.4k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
5 months ago Elizabeth • 0
0
votes
2
replies
652
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 5 months ago by 43k • written 5 months ago by ▴ 20
0
votes
1
reply
383
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 6 months ago by 52k • written 6 months ago by • 0
0
votes
4
replies
1.3k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 5 months ago by • 0 • written 6 months ago by • 0
2
votes
4
replies
810
views
EdgeR Biological CVs
edgeR
written 7 months ago by • 0
3
votes
5
replies
1.8k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 7 months ago by 68k • written 7 months ago by ▴ 10
0
votes
2
replies
575
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
7 months ago gingergeiger22 • 0
0
votes
1
reply
549
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 8 months ago by 43k • written 8 months ago by • 0
1
vote
8
replies
1.4k
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
8 months ago • updated 7 months ago Andre • 0
1
vote
9
replies
1.3k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 8 months ago by ▴ 30
6
votes
10
replies
3.2k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 8 months ago by ★ 4.9k • written 9 months ago by ▴ 10
7
votes
6
replies
1.3k
views
ANOVA like approach of edgeR
edgeR
updated 9 months ago by 52k • written 9 months ago by ▴ 10
3
votes
3
replies
837
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 9 months ago by 52k • written 9 months ago by • 0
2
votes
4
replies
2.3k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 9 months ago by 52k • written 9 months ago by • 0
1
vote
8
replies
2.3k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 10 months ago by • 0
0
votes
1
reply
817
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 10 months ago by 68k • written 10 months ago by • 0
3
votes
3
replies
1.4k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 10 months ago by • 0
0
votes
4
replies
950
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
10 months ago Philippine • 0
4
votes
6
replies
1.6k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
10 months ago altintas.ali • 0
1
vote
2
replies
624
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
10 months ago Hongjian • 0
3
votes
3
replies
649
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
10 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
597
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 10 months ago by 52k • written 10 months ago by • 0
1
vote
1
reply
501
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 11 months ago by ★ 4.9k • written 11 months ago by • 0
1
vote
2
replies
785
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 11 months ago by 43k • written 11 months ago by ▴ 10
0
votes
2
replies
707
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 11 months ago by 52k • written 11 months ago by • 0
1
vote
2
replies
621
views
Inconsistent result in edgeR
edgeR
11 months ago hiroko.ohmiya • 0
1
vote
1
reply
782
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 11 months ago by 52k • written 12 months ago by • 0
2
votes
9
replies
1.3k
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 12 months ago by 52k • written 12 months ago by • 0
0
votes
3
replies
934
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 12 months ago by • 0
1
vote
1
reply
2.0k
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 12 months ago by ★ 29k • written 12 months ago by • 0
0
votes
1
reply
677
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 12 months ago by 52k • written 12 months ago by • 0
3
votes
3
replies
963
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 12 months ago by 68k • written 13 months ago by ▴ 60
0
votes
4
replies
976
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 13 months ago by • 0
1
vote
8
replies
1.7k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 13 months ago by 52k • written 14 months ago by • 0
3
votes
5
replies
3.1k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 14 months ago by • 0 • written 18 months ago by ▴ 60
0
votes
4
replies
1.0k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
14 months ago vohara4 • 0
3
votes
6
replies
1.2k
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
15 months ago JG13 • 0
2,027 results • Page 1 of 41
Recent ...
Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
Awards • All
Popular Question to Robert Castelo ★ 3.4k
Popular Question to Gordon Smyth 52k
Popular Question to littlefishes20 ▴ 10
Popular Question to Dario Strbenac ★ 1.6k
Popular Question to shepherl 4.2k
Locations • All
WEHI, Melbourne, Australia, 36 minutes ago
India, 2 hours ago
United States, 2 hours ago
Barcelona, Spain, 8 hours ago
The city by the bay, 8 hours ago
Traffic: 975 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