Notes

This page is mostly for myself as a notekeeping place.

*nix note

Linux

BSD

R notes

• Transform between Seurat v5 and v3 Assay objects (ref):

  # convert a v5 assay to a v3 assay
  seurat_obj[['RNA3']] <- as(object = seurat_obj[['RNA']], Class = 'Assay')
  
  # convert a v3 assay to a v5 assay
  seurat_obj[['RNA5']] <- as(object = seurat_obj[['RNA3']], Class = 'Assay5')
  

• R/Bioconductor: Genome and Annoation

  • GenomicFeatures: Obtaining and Utilizing TxDb Objects
  • ensembldb: Generating and using Ensembl based annotation packages
  • BSgenome: Software infrastructure for efficient representation of full genomes and their SNPs
  • org.Mm.eg.db: Genome wide annotation for Mouse, primarily based on mapping using Entrez Gene identifiers.
  • Ensembl: Table of Assemblies