Showing : edger • reset
2
votes
4
replies
1.5k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 8 days ago by 51k • written 12 days ago by • 0
1
vote
8
replies
956
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 14 days ago by • 0
0
votes
1
reply
419
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 17 days ago by 67k • written 17 days ago by • 0
3
votes
3
replies
820
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 23 days ago by • 0
0
votes
4
replies
547
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
24 days ago • updated 22 days ago Philippine • 0
4
votes
6
replies
1.0k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
4 weeks ago • updated 23 days ago altintas.ali • 0
1
vote
2
replies
286
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
4 weeks ago Hongjian • 0
3
votes
3
replies
275
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
5 weeks ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
294
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 5 weeks ago by 51k • written 6 weeks ago by • 0
1
vote
1
reply
225
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 7 weeks ago by ★ 4.5k • written 7 weeks ago by • 0
1
vote
2
replies
431
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 7 weeks ago by 42k • written 8 weeks ago by ▴ 10
0
votes
2
replies
325
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 7 weeks ago by 51k • written 7 weeks ago by • 0
1
vote
2
replies
301
views
Inconsistent result in edgeR
edgeR
8 weeks ago hiroko.ohmiya • 0
1
vote
1
reply
417
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 10 weeks ago by 51k • written 10 weeks ago by • 0
2
votes
9
replies
779
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 11 weeks ago by 51k • written 12 weeks ago by • 0
0
votes
3
replies
475
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 3 months ago by • 0
1
vote
1
reply
587
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 3 months ago by ★ 28k • written 3 months ago by • 0
0
votes
1
reply
352
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 3 months ago by 51k • written 3 months ago by • 0
3
votes
3
replies
541
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 3 months ago by 67k • written 3 months ago by ▴ 50
0
votes
4
replies
549
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 4 months ago by • 0
1
vote
8
replies
916
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 4 months ago by 51k • written 4 months ago by • 0
3
votes
5
replies
1.5k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 5 months ago by • 0 • written 8 months ago by ▴ 50
0
votes
4
replies
572
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
5 months ago vohara4 • 0
3
votes
6
replies
806
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
5 months ago JG13 • 0
3
votes
2
replies
620
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
6 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
671
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 6 months ago by 51k • written 6 months ago by • 0
1
vote
3
replies
614
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 6 months ago by 51k • written 6 months ago by • 0
0
votes
1
reply
373
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 6 months ago by 51k • written 6 months ago by • 0
4
votes
2
replies
1.1k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
6 months ago gene_bioconductor ▴ 10
1
vote
2
replies
693
views
Citation for edgeR user guide
edgeR
written 6 months ago by ▴ 30
4
votes
6
replies
969
views
FilterByExpr low counts with small sample size
edgeR
7 months ago Jonathan ▴ 10
0
votes
2
replies
368
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
7 months ago prity6459 • 0
0
votes
3
replies
544
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 7 months ago by 51k • written 7 months ago by • 0
5
votes
3
replies
821
views
Log-cpm values from limma
limma edgeR RNASeq
updated 6 months ago by 51k • written 7 months ago by • 0
3
votes
3
replies
844
views
permutation test in edgeR
rna-seq edgeR
updated 7 months ago by 51k • written 7 months ago by • 0
1
vote
3
replies
621
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 7 months ago by 51k • written 7 months ago by • 0
5
votes
6
replies
846
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 7 months ago by ★ 4.5k • written 7 months ago by ▴ 70
1
vote
3
replies
541
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 7 months ago by 67k • written 7 months ago by • 0
0
votes
2
replies
505
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
7 months ago Marianna ▴ 20
0
votes
4
replies
817
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
7 months ago Lucy ▴ 60
3
votes
5
replies
1.1k
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 7 months ago by 51k • written 7 months ago by • 0
0
votes
6
replies
695
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 7 months ago by 51k • written 7 months ago by • 0
0
votes
1
reply
553
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 8 months ago by 51k • written 8 months ago by • 0
6
votes
5
replies
1.7k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 20 days ago by 51k • written 8 months ago by ▴ 50
2
votes
3
replies
567
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 8 months ago by 51k • written 8 months ago by • 0
0
votes
2
replies
559
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 months ago by 51k • written 8 months ago by • 0
2
votes
2
replies
532
views
between lane normalization upper quantile
EDASeq edgeR
8 months ago elesofi • 0
2
votes
2
replies
503
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
8 months ago Sabiha ▴ 20
1
vote
3
replies
706
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 9 months ago by • 0
0
votes
1
reply
398
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 8 months ago by 51k • written 8 months ago by • 0
50 results • Page 1 of 1
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Comment: preprocessIllumina error with EPICv2 array by Rakesh • 0
Amazing, thanks for the help!
Answer: Allele frequencies for ALL alleles of one SNP ? by Robert Castelo ★ 3.4k
Hi, the [GenomicScores](https://bioconductor.org/packages/GenomicSCores) package provides supporting infrastructure to create annotation re…
Answer: preprocessIllumina error with EPICv2 array by James W. MacDonald 67k
You shouldn't need to change the annotation, and certainly not like that. You should never need to use the `@` function directly - there ar…
Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data by Haibo Liu • 0
Thank you for your reminder. I did forget that, but I just bumped the version to 1.1.1.
Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data by shepherl 4.1k
@haibol2017-23658 make sure you have the valid version bump in the description on our git repository in order for the new version to propa…
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Answer: preprocessIllumina error with EPICv2 array
Answer: preprocessIllumina error with EPICv2 array
Answer: UniProt.ws query loading indefinitely
Answer: Package needs internet access
Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
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