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1 month, 3 weeks ago
United States
Non-monotonic voomByGroup plot in Xenium data
1 month, 4 weeks ago
United States
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
2 months ago
United States
competitive enrichment test yields too few significant results, self-contained too many
2 months ago
Switzerland
Best practice for handling large data (matrix with >2^31-1 non-zero elements) in SingleCellExperiment?
2 months, 1 week ago
Hong Kong
I would like to perform differential expression analysis of lncRNAs using DESeq2 and edgeR.
2 months, 3 weeks ago
United States
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
2 months, 3 weeks ago
Germany
Analysis of clusters of a heatmap with enrichGO of clusterProfiler: choice fo the categories to visualize
2 months, 3 weeks ago
United States
Is voomByGroup available in limma?
3 months ago
United States
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
3 months, 1 week ago
Italy
Deseq2 paired sample in the design is considered as "batch"?
3 months, 1 week ago
United States
limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
3 months, 2 weeks ago
India
ERCC Spike-In controls being discarded during Tximeta process:
3 months, 2 weeks ago
United States
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
3 months, 2 weeks ago
India
Altered (negative or positive) logFC values for same gene from two intitial count matrices, one being a subset of the other
3 months, 2 weeks ago
Italy
Possible issue following the logNormCounts(filtered) with resulted fit
3 months, 3 weeks ago
Germany
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
3 months, 3 weeks ago
United Kingdom
Discrepancies in normalised count data vs unnormalised
3 months, 3 weeks ago
Ireland
Announcing GBCC 2025: The first-ever joint conference between Bioconductor and Galaxy!
4 months, 1 week ago
United States
DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
4 months, 2 weeks ago
United States
edgeR::cpm() results in negative values from raw counts of 0
4 months, 4 weeks ago
United States
Support of parquet files for on-disk Bioconductor objects
5 months ago
Canada
Origin of the labels for the SingleCellMultiModal dataset
5 months, 1 week ago
United Kingdom
DESeq: Gene is not flagged as differentially expressed despite count data showing differences
5 months, 1 week ago
United Kingdom
Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
5 months, 2 weeks ago
United States
Package developing and interoperation with Bioconductor
5 months, 3 weeks ago
United Kingdom
Using TPM from tximport of Salmon output for singscore
5 months, 4 weeks ago
France
Limma - Complex 2-way multi-level contrast with paired samples
6 months, 1 week ago
United States
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
6 months, 1 week ago
Germany/Heidelberg/German Cancer Resear…
Use of limma R package with targeted proteomics for DE analysis
6 months, 2 weeks ago
USA
Group-specific condition effects with individuals nested: matrix is not full rank
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