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
733
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
500
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
706
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
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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?
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