Showing : edgeR • reset
2
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9
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509
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Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
24 days ago • updated 22 days ago mohammedtoufiq91 ▴ 10
3
votes
2
replies
741
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Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
5 weeks ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
835
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 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 bbao ▴ 10
5
votes
11
replies
2.9k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 4 months ago by ▴ 10
2
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4
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2.5k
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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
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3
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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
778
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
873
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 4 months ago by ▴ 10
10
votes
13
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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
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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
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653
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 5 months ago by 43k • written 5 months ago by ▴ 20
0
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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 6 months ago by • 0 • written 6 months ago by • 0
2
votes
4
replies
811
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
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575
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
8 months ago • updated 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
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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
838
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 10 months ago by • 0
1
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8
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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
819
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
953
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
10 months ago Philippine • 0
4
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6
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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
626
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
10 months ago Hongjian • 0
3
votes
3
replies
650
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
10 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
599
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 10 months ago by 52k • written 11 months ago by • 0
1
vote
1
reply
502
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
790
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
710
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
626
views
Inconsistent result in edgeR
edgeR
11 months ago hiroko.ohmiya • 0
1
vote
1
reply
783
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 12 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
937
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 13 months ago by ★ 29k • written 13 months ago by • 0
0
votes
1
reply
680
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 13 months ago by 52k • written 13 months ago by • 0
3
votes
3
replies
963
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 13 months ago by 68k • written 13 months ago by ▴ 60
0
votes
4
replies
980
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 14 months ago by • 0
1
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8
replies
1.7k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 14 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: WGCNA analysis on RNAseq and proteoimcs data by sum31278 • 0
Hi sagigordon, Can you share how you performed WGCNA analysis for proteomics data? Thanks
Comment: European Bioconductor Conference 2023 planning by inadequate.peacock.iiag • 0
I once faced a dilemma similar to this when coordinating a smaller local event; despite initial hesitation, I learned invaluable skills and…
Comment: ROAST compare results with complex design by Gordon Smyth 52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Votes
Answer: ROAST compare results with complex design
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
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