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Created An Answer That Has Been Accepted
Awarded 5103 times (see all awards). Earned by the
following contributors:
3 weeks, 3 days ago
WEHI, Melbourne, Australia
Answer: Limma-voom sample weights and impact on DEG numbers
1 month, 3 weeks ago
WEHI, Melbourne, Australia
Answer: Large logFC but somewhat high FDR
2 months ago
WEHI, Melbourne, Australia
Answer: Identifying differentially expressed genes in individual samples from a large co
2 months ago
WEHI, Melbourne, Australia
Answer: Post translational modifications and phosphoproteomics in limpa?
2 months, 1 week ago
United States
Answer: Failure to download resources (MeSHDb) from AnnotationHub
4 months ago
WEHI, Melbourne, Australia
Answer: replace cat with message in glmTreat when lfc = 0
4 months, 1 week ago
WEHI, Melbourne, Australia
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
5 months, 2 weeks ago
WEHI, Melbourne, Australia
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
5 months, 2 weeks ago
United States
Answer: makeChipPackage(): Error in data.frame(..., check.names = FALSE) : arguments
5 months, 2 weeks ago
WEHI, Melbourne, Australia
Answer: Limma : paired samples leading to unexpected estimates
5 months, 3 weeks ago
WEHI, Melbourne, Australia
Answer: Transcript expression analysis using EdgeR
7 months, 2 weeks ago
United States
Answer: DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
7 months, 2 weeks ago
Germany
Answer: Deseq2 paired sample in the design is considered as "batch"?
7 months, 2 weeks ago
WEHI, Melbourne, Australia
Answer: limma duplicateCorrelation appropriate where some blocks cross condition and som
8 months ago
United States
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
8 months, 1 week ago
Seattle, WA, United States
Answer: GAlignments Cigar to GRanges
8 months, 1 week ago
United States
Answer: AnnotationHub/ExperimentHub resources backup
8 months, 1 week ago
United States
Answer: DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
9 months, 1 week ago
WEHI, Melbourne, Australia
Answer: how to use `arrayWeightsQuick()`?
9 months, 2 weeks ago
Germany
Answer: Origin of the labels for the SingleCellMultiModal dataset
10 months ago
United States
Answer: Using TPM from tximport of Salmon output for singscore
10 months ago
WEHI, Melbourne, Australia
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
10 months, 1 week ago
United States
Answer: Limma - Complex 2-way multi-level contrast with paired samples
10 months, 1 week ago
United States
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
10 months, 2 weeks ago
United States
Answer: Surprising behavior for DEXseq dispersion estimate plot?
10 months, 3 weeks ago
United States
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
11 months ago
The city by the bay
Answer: SingleR with multiple single cell references
11 months, 2 weeks ago
United States
Answer: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode =
11 months, 2 weeks ago
United States
Answer: Find exact GRanges match keeping metadata columns
11 months, 3 weeks ago
Barcelona, Spain
Answer: Unused arguments error without used arguments in GSVA?
11 months, 3 weeks ago
The city by the bay
Answer: Csaw normalization strategies - general inquiry
1 year ago
United States
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
1 year ago
United States
Answer: Is it possible to work with DESeq2 where data is not properly matched for sex a
1 year, 1 month ago
Germany
Answer: Standardization of rlog transformed counts before PCA
1 year, 1 month ago
United States
Answer: Standardization of rlog transformed counts before PCA
1 year, 1 month ago
WEHI, Melbourne, Australia
Answer: RSubread output significantly different from bash Subread output
1 year, 1 month ago
The city by the bay
Answer: Running multiple KNN queries in parallel
1 year, 1 month ago
Germany
Answer: RSubread output significantly different from bash Subread output
1 year, 1 month ago
United States
Answer: Struggle with the replicates of epic array data
1 year, 1 month ago
WEHI, Melbourne, Australia
Answer: Is it recommended to analyze different tissues together when using edgeR
1 year, 1 month ago
United States
Answer: preprocessIllumina error with EPICv2 array
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