Pinned Loading

1. MasteringShiny MasteringShiny Public

   R

2. sjmatkovich.github.io sjmatkovich.github.io Public

   JavaScript

3. Limma differential gene expression, ... Limma differential gene expression, without empirical Bayes moderation

   1

   # A *limma* workflow without empirical Bayes moderation of t-statistics

   2

   3

   **Situation:** You are preparing differential gene expression calculations with the R/Bioconductor *limma* package (including RNA-sequencing extensions such as *limma-voom*). While *limma* offers empirical Bayes moderation of t-statistics ('borrowing' variance estimates across genes), you have a large number of individual samples or have other reasons to avoid this procedure.

   4

   5

   **Problem:** Omitting the `eBayes` step in the limma workflow means that t-statistics are not calculated, and the useful `topTable` function of the package to summarize differential expression calculations does not function.

4. hbctraining_scRNA-seq_online hbctraining_scRNA-seq_online Public

   Forked from hbctraining/scRNA-seq_online

   Harvard Chan bioinformatics core scRNAseq workshop - with custom & Seurat > v5.0 code

   R

5. Seurat_walkthroughs Seurat_walkthroughs Public

   Code and notes to follow tutorials and vignettes on Seurat website

   HTML