This directory contains some files describing the HVG detection machinery in scran. In theory/:

• description.tex focuses on the theoretical basis behind trendVar and decomposeVar.
• comparison.tex considers the differences between the possible HVG detection methods in scran.

In real/:

• fitTrendVar_test.Rmd tests the behaviour of the fitTrendVar() on a range of scenarios.
• fitTrendCV2_test.Rmd tests the behaviour of the fitTrendCV2() on a range of scenarios.

In simulations/:

• power contains simulation scripts to compare the performance of decomposeVar with technicalCV2 and improvedCV2 for detecting HVGs. Each simulation script describes a different type of variability, though this is not particularly important for gene-wise testing.
• alpha assesses the type I error rate for the tests in decomposeVar, technicalCV2 and improvedCV2.
• filter examines the motivation for the default filter threshold in trendVar.