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following contributors:
1 month, 3 weeks ago
WEHI, Melbourne, Australia
Answer: edgeR 4.2.1 compression bug: a minimally reproducible snippet
5 months, 1 week ago
WEHI, Melbourne, Australia
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
7 months ago
WEHI, Melbourne, Australia
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
9 months, 3 weeks ago
WEHI, Melbourne, Australia
Answer: How does one test for interactions in EdgeR?
9 months, 3 weeks ago
WEHI, Melbourne, Australia
Answer: Design matrix after RUVg correction
10 months, 2 weeks ago
WEHI, Melbourne, Australia
Answer: Monotonic genes in results of differential gene expression analysis
1 year, 1 month ago
WEHI, Melbourne, Australia
Answer: DecideTest vs topTAGs in edgeR
1 year, 2 months ago
WEHI, Melbourne, Australia
Answer: Batch correction and repeated measures
1 year, 2 months ago
WEHI, Melbourne, Australia
Answer: Phenotype effect - building a contrast matrix - grouping vs interaction
1 year, 4 months ago
WEHI, Melbourne, Australia
Answer: ASpli checks fail on Linux due to missing dependency to statmod
1 year, 11 months ago
WEHI, Melbourne, Australia
Answer: How to identify top most variable genes from log2 normalized data?
2 years, 6 months ago
WEHI, Melbourne, Australia
Answer: Pseudo-bulk Limma Approaches
2 years, 8 months ago
WEHI, Melbourne, Australia
Answer: GSEA many significant gene sets despite no differentially expressed genes
3 years ago
WEHI, Melbourne, Australia
Answer: Using edgeR and a spike-in to calculate absolute abundance
3 years, 3 months ago
WEHI, Melbourne, Australia
Answer: Query regarding the use of eBayes + topTable and treat + topTreat
3 years, 3 months ago
WEHI, Melbourne, Australia
Answer: Query regarding the use of eBayes + topTable and treat + topTreat
3 years, 8 months ago
WEHI, Melbourne, Australia
A: Effect size similar to Cohen's d in limma
3 years, 8 months ago
WEHI, Melbourne, Australia
Answer: Weird MAplot with DEGs lying along the diagonals
3 years, 9 months ago
WEHI, Melbourne, Australia
Answer: Why some statistically differently expressed genes are not DEGs?
3 years, 9 months ago
WEHI, Melbourne, Australia
Answer: Getting differentially expressed genes for time points
4 years, 1 month ago
WEHI, Melbourne, Australia
Answer: How to get gene length for RPKM directly from DGEList object in latest edgeR?
4 years, 2 months ago
WEHI, Melbourne, Australia
A: Comparing DEseq2 and Limma program, results not consistent
4 years, 2 months ago
WEHI, Melbourne, Australia
A: Differential gene expression associated with change in blood parameter following
4 years, 2 months ago
WEHI, Melbourne, Australia
A: TMM normalization on sparse datasets
4 years, 3 months ago
WEHI, Melbourne, Australia
A: Moderated F-test followed by moderated t-test in limma
4 years, 6 months ago
WEHI, Melbourne, Australia
A: edgeR Time course analysis, choice on degree of freedom
4 years, 6 months ago
WEHI, Melbourne, Australia
A: Suggestion for next revision of edgeR User Guide re Design matrix setup
4 years, 6 months ago
WEHI, Melbourne, Australia
A: linear mixed models using edgeR+limma
4 years, 6 months ago
WEHI, Melbourne, Australia
A: Multi-level experiments in Limma
4 years, 8 months ago
WEHI, Melbourne, Australia
A: How to know if I should use voomWithQualityWeights() or not?
4 years, 9 months ago
WEHI, Melbourne, Australia
A: Correcting for tissue purity in differential expression analysis
4 years, 10 months ago
WEHI, Melbourne, Australia
A: How to deal with elimination of genes when using filterByExpr function?
4 years, 11 months ago
WEHI, Melbourne, Australia
A: Can I use (length bias normalization) from packages like EDAseq or cqn for input
5 years, 1 month ago
WEHI, Melbourne, Australia
A: Account for inter individual variability at the baseline using nested models
5 years, 1 month ago
WEHI, Melbourne, Australia
A: Bug in estimateDisp of "edgeR"? "weights' matched by multiple actual arguments
5 years, 2 months ago
WEHI, Melbourne, Australia
A: RNASeq DE analysis starts from different DESeq2 normalized data, TMM normalized
5 years, 3 months ago
WEHI, Melbourne, Australia
Rsubread, Error in featureCounts paired end
5 years, 3 months ago
WEHI, Melbourne, Australia
Rsubread, Error in featureCounts paired end
5 years, 3 months ago
WEHI, Melbourne, Australia
A: the normalization methods of MRN and TMM methods supplied by DESeq2 and edgeR
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