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Criticisms of MAGIC in scRNA-seq data

This repository contains code to explore some of the consequences of using MAGIC in scRNA-seq data. The report subdirectory contains LaTeX files for the report, which you can compile yourself if you know how. The scripts subdirectory contains R code to reproduce the analyses described in the report:

  • nostruct_sim.R, to examine the effect of using MAGIC in a simulation without any structure.
  • structloss_sim.R, involving a simulation containing primary and secondary separations.
  • fakede_sim.R, involving DE analysis between two well-separated subpopulations.
  • run_ercc.R, to examine the effect of using MAGIC on the ERCC data set from 10X Genomics.
  • run_293t.R, to examine the effect of using MAGIC on the 293T data set from 10X Genomics.
  • run_tb.R, to test behaviour when combining B and T cells.