Large-scale clustering in Bioconductor

Key resources

Demo description

This website gives a demo of large-scale clustering in the Bioconductor using the DelayedArray framework. DelayedArray is like an ordinary array in R, but allows for the data to be in-memory, on-disk in a file, or even hosted on a remote server. Specifically, we present two forms of dimensionality reduction :

  1. scran normalization + PCA
  2. glmpca with scry

Using these reduced dimensions, we present two types of clustering:

  1. SNN + Louvain clustering
  2. mini-batch k-means (mbkmeans)

R / Bioconductor packages used

These packages are the focus of this workshop:

  • SingleCellExperiment
  • TENxPBMCData
  • scater
  • scran
  • scry
  • mbkmeans

Please see the workshop DESCRIPTION for a full list of dependencies.

Installation

This demo uses Bioconductor version 3.12. This is the current ‘release’ version of Bioconductor, which can be installed following these instructions.

You can then install the packages necessary for this workshop using the following:

library(BiocManager)
install(c("SingleCellExperiment", "TENxPBMCData", "scater", "scran",
  "scry", "mbkmeans"))