Showing : edger • reset
0
votes
2
replies
622
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 7 days ago by ★ 4.8k • written 8 days ago by • 0
5
votes
3
replies
764
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 14 days ago by 52k • written 15 days ago by ▴ 10
2
votes
2
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1.1k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
22 days ago • updated 16 days ago Elizabeth • 0
0
votes
2
replies
419
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 16 days ago by 43k • written 24 days ago by ▴ 20
0
votes
1
reply
238
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 29 days ago by 52k • written 29 days ago by • 0
0
votes
4
replies
1.1k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 28 days ago by • 0 • written 4 weeks ago by • 0
2
votes
4
replies
583
views
EdgeR Biological CVs
edgeR
written 10 weeks ago by • 0
3
votes
5
replies
1.3k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 10 weeks ago by 68k • written 10 weeks ago by ▴ 10
0
votes
2
replies
357
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
12 weeks ago gingergeiger22 • 0
0
votes
1
reply
422
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 12 weeks ago by 43k • written 3 months ago by • 0
1
vote
8
replies
1.1k
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
3 months ago • updated 12 weeks ago Andre • 0
1
vote
9
replies
998
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 3 months ago by ▴ 30
6
votes
10
replies
2.8k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 3 months ago by ★ 4.8k • written 4 months ago by ▴ 10
7
votes
6
replies
1.1k
views
ANOVA like approach of edgeR
edgeR
updated 4 months ago by 52k • written 4 months ago by ▴ 10
3
votes
3
replies
655
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 4 months ago by 52k • written 4 months ago by • 0
2
votes
4
replies
1.9k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 4 months ago by 52k • written 4 months ago by • 0
1
vote
8
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1.7k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 4 months ago by • 0
0
votes
1
reply
621
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 5 months ago by 68k • written 5 months ago by • 0
3
votes
3
replies
1.1k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 5 months ago by • 0
0
votes
4
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776
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
5 months ago Philippine • 0
4
votes
6
replies
1.4k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
5 months ago altintas.ali • 0
1
vote
2
replies
439
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
5 months ago Hongjian • 0
3
votes
3
replies
444
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
5 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
461
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 5 months ago by 52k • written 5 months ago by • 0
1
vote
1
reply
364
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 6 months ago by ★ 4.8k • written 6 months ago by • 0
1
vote
2
replies
617
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 6 months ago by 43k • written 6 months ago by ▴ 10
0
votes
2
replies
523
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 6 months ago by 52k • written 6 months ago by • 0
1
vote
2
replies
467
views
Inconsistent result in edgeR
edgeR
6 months ago hiroko.ohmiya • 0
1
vote
1
reply
588
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 6 months ago by 52k • written 7 months ago by • 0
2
votes
9
replies
1.0k
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 7 months ago by 52k • written 7 months ago by • 0
0
votes
3
replies
713
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 7 months ago by • 0
1
vote
1
reply
1.3k
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 7 months ago by ★ 28k • written 7 months ago by • 0
0
votes
1
reply
490
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 7 months ago by 52k • written 7 months ago by • 0
3
votes
3
replies
722
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 7 months ago by 68k • written 7 months ago by ▴ 60
0
votes
4
replies
756
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 8 months ago by • 0
1
vote
8
replies
1.3k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 8 months ago by 52k • written 9 months ago by • 0
3
votes
5
replies
2.5k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 9 months ago by • 0 • written 13 months ago by ▴ 60
0
votes
4
replies
783
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
9 months ago vohara4 • 0
3
votes
6
replies
1.0k
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
10 months ago JG13 • 0
3
votes
2
replies
853
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
10 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
897
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 10 months ago by 52k • written 10 months ago by • 0
1
vote
3
replies
802
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 10 months ago by 52k • written 10 months ago by • 0
0
votes
1
reply
472
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 11 months ago by 52k • written 11 months ago by • 0
4
votes
2
replies
1.4k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
11 months ago gene_bioconductor ▴ 10
1
vote
2
replies
1.1k
views
Citation for edgeR user guide
edgeR
written 11 months ago by ▴ 30
4
votes
6
replies
1.3k
views
FilterByExpr low counts with small sample size
edgeR
11 months ago Jonathan ▴ 10
0
votes
2
replies
478
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
11 months ago prity6459 • 0
0
votes
3
replies
730
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 11 months ago by 52k • written 11 months ago by • 0
5
votes
3
replies
1.2k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 10 months ago by 52k • written 11 months ago by • 0
3
votes
3
replies
1.3k
views
permutation test in edgeR
rna-seq edgeR
updated 11 months ago by 52k • written 11 months ago by • 0
50 results • Page 1 of 1
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Comment: Issue with Soft-Thresholding in WGCNA by dirty.cougar.risi • 0
Interesting data! Looking at these genes, it's like navigating a complex maze. The fluctuating values remind me of chasing high scores in […
Answer: compute_fasta_digest does not match Salmon index hash by Michael Love 43k
Can you provide more details on when this is happening? The salmon index is the definitive hash associated with the quant files, so I'm con…
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species by James W. MacDonald 68k
Oh wait. You want to map from Ensembl to NCBI? That's hard to do with model organisms, let alone non-model. This `OrgDb` doesn't have Ensem…
Answer: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species by James W. MacDonald 68k
You can use the `AnnotationHub` ``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% sna…
Answer: List of Deprecated Packages for Bioc3.20 by shepherl 4.1k
HTqPCR has been fixed and will be re-instated in 3.21
Votes
what the test method for enrichGO in clusterProfiler?
A: single-cells RNA-seq analysis by MAST with unbalanced group size
Comment: plyranges: find exact GRanges match keeping metadata columns
Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran
Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?
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