Showing : EdgeR • reset
0
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3
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674
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Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 5 weeks ago by ▴ 10
1
vote
5
replies
824
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
updated 8 days ago by 52k • written 11 days ago by • 0
10
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13
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1.8k
views
edgeR::cpm() results in negative values from raw counts of 0
edgeR
updated 20 days ago by 52k • written 22 days ago by ▴ 20
2
votes
2
replies
1.2k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 6 weeks ago by ★ 4.8k • written 7 weeks ago by • 0
5
votes
3
replies
871
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 7 weeks ago by 52k • written 7 weeks ago by ▴ 10
2
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2
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1.2k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
9 weeks ago • updated 8 weeks ago Elizabeth • 0
0
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2
replies
493
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 8 weeks ago by 43k • written 9 weeks ago by ▴ 20
0
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1
reply
284
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 10 weeks ago by 52k • written 10 weeks ago by • 0
0
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4
replies
1.2k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 9 weeks ago by • 0 • written 10 weeks ago by • 0
2
votes
4
replies
673
views
EdgeR Biological CVs
edgeR
written 3 months ago by • 0
3
votes
5
replies
1.5k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 3 months ago by 68k • written 3 months ago by ▴ 10
0
votes
2
replies
423
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
4 months ago gingergeiger22 • 0
0
votes
1
reply
456
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 4 months ago by 43k • written 4 months ago by • 0
1
vote
8
replies
1.2k
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
4 months ago Andre • 0
1
vote
9
replies
1.1k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 4 months ago by ▴ 30
6
votes
10
replies
3.0k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 5 months ago by ★ 4.8k • written 5 months ago by ▴ 10
7
votes
6
replies
1.1k
views
ANOVA like approach of edgeR
edgeR
updated 5 months ago by 52k • written 5 months ago by ▴ 10
3
votes
3
replies
708
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 5 months ago by 52k • written 5 months ago by • 0
2
votes
4
replies
2.1k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 6 months ago by 52k • written 6 months ago by • 0
1
vote
8
replies
2.0k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 6 months ago by • 0
0
votes
1
reply
708
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 6 months ago by 68k • written 6 months ago by • 0
3
votes
3
replies
1.2k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 6 months ago by • 0
0
votes
4
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822
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
6 months ago Philippine • 0
4
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6
replies
1.5k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
6 months ago altintas.ali • 0
1
vote
2
replies
491
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
6 months ago Hongjian • 0
3
votes
3
replies
499
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
7 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
504
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 7 months ago by 52k • written 7 months ago by • 0
1
vote
1
reply
397
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 7 months ago by ★ 4.8k • written 7 months ago by • 0
1
vote
2
replies
666
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 7 months ago by 43k • written 7 months ago by ▴ 10
0
votes
2
replies
585
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 7 months ago by 52k • written 7 months ago by • 0
1
vote
2
replies
508
views
Inconsistent result in edgeR
edgeR
7 months ago hiroko.ohmiya • 0
1
vote
1
reply
667
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 8 months ago by 52k • written 8 months ago by • 0
2
votes
9
replies
1.1k
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 8 months ago by 52k • written 8 months ago by • 0
0
votes
3
replies
795
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 9 months ago by • 0
1
vote
1
reply
1.7k
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 9 months ago by ★ 28k • written 9 months ago by • 0
0
votes
1
reply
540
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 9 months ago by 52k • written 9 months ago by • 0
3
votes
3
replies
803
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 9 months ago by 68k • written 9 months ago by ▴ 60
0
votes
4
replies
824
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 10 months ago by • 0
1
vote
8
replies
1.5k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 10 months ago by 52k • written 10 months ago by • 0
3
votes
5
replies
2.8k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 months ago by • 0 • written 14 months ago by ▴ 60
0
votes
4
replies
841
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
11 months ago vohara4 • 0
3
votes
6
replies
1.0k
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
11 months ago JG13 • 0
3
votes
2
replies
924
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
11 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
984
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 12 months ago by 52k • written 12 months ago by • 0
1
vote
3
replies
855
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 12 months ago by 52k • written 12 months ago by • 0
0
votes
1
reply
502
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 12 months ago by 52k • written 12 months ago by • 0
4
votes
2
replies
1.5k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
12 months ago gene_bioconductor ▴ 10
1
vote
2
replies
1.3k
views
Citation for edgeR user guide
edgeR
written 12 months ago by ▴ 30
4
votes
6
replies
1.4k
views
FilterByExpr low counts with small sample size
edgeR
13 months ago • updated 12 months ago Jonathan ▴ 10
0
votes
2
replies
530
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
12 months ago prity6459 • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change by James W. MacDonald 68k
Yes, you can simply flip the sign of the logFC to reverse the direction of the comparison.
Comment: Heatmap of a transformed deseq object with pheatmap by James W. MacDonald 68k
The argument for annotation_col is meant to be a `data.frame`, not a vector. The hint in the error is that it has the wrong number of dimen…
Comment: Heatmap of a transformed deseq object with pheatmap by caroline.zanchi • 0
I used this argument in the second paragraph of code forthe heatmap, this is wehre I got the message Error in `[.default`(annotation_col, c…
Answer: Heatmap of a transformed deseq object with pheatmap by James W. MacDonald 68k
Ah, yes. The non-ASCII character error. My favorite! Please note that `pheatmap` is not a Bioconductor package, so you should be asking …
Comment: Heatmap of a transformed deseq object with pheatmap by caroline.zanchi • 0
It is in ! It just took longer than planned :) ... aaaand now that I added the heatmap in I realize lits of genes really do not look like t…
Votes
Comment: Heatmap of a transformed deseq object with pheatmap
DESeq2: Question about the alpha in summary() and results()
Comment: How to load scRNA-seq data from GEO
limma correction for tumor purity
limma correction for tumor purity
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