Bioconductor EnsDb

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Ensembl Rstudio ensembldb AnnotationHub ensdb

updated 6 months ago by shepherl 4.1k • written 3.0 years ago by jon.klonowski ▴ 40

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EnsDb ensembldb annotation AnnotationHub News

4.4 years ago Johannes Rainer ★ 2.1k

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annotation ensembldb EnsDb AnnotationHub News

5.2 years ago Johannes Rainer ★ 2.1k

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GRanges ChIPseeker annotatePeak TxDb EnsDb

updated 5.9 years ago by Johannes Rainer ★ 2.1k • written 5.9 years ago by foehn ▴ 100

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Comment: contrast matrix design for a continuous variable by dtzhu337 • 0

Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…

Answer: SingleCellExperiment convenience function for metadata+expression? by Peter Hickey ▴ 740

Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…

Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10

Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…

Comment: EdgeR Biological CVs by ATpoint ★ 4.6k

"Joseph" is a spam bot...

Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k

GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…

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How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.

Answer: EdgeR Biological CVs

Answer: Error in download.file for TCGAutils::symbolsToRanges

Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?

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