Installation

Requirements

• R >= 3.5

• Biobase — sc and bulk inputs to climb() are ExpressionSet objects

• glmnet — underlying linear/EM model fitting

• reshape2 — used internally by cliff()

ClimbTheCliff calls functions from these packages directly without re-exporting them, so attach them yourself before calling climb() or cliff():

library(Biobase)
library(glmnet)
library(reshape2)
library(ClimbTheCliff)

From GitHub

Using devtools:

install.packages("devtools")
devtools::install_github("alexdray86/ClimbTheCliff", force = TRUE)

Using remotes:

install.packages("remotes")
remotes::install_github("alexdray86/ClimbTheCliff", force = TRUE)

force = TRUE ensures a fresh reinstall even if a previous copy is already present — the package’s DESCRIPTION version does not change between releases, so devtools/remotes cannot tell from the version number alone that an update is available.

Installing a specific version

To pin a specific frozen release instead of main, pass its tag as ref:

devtools::install_github("alexdray86/ClimbTheCliff", ref = "1.1.0", force = TRUE)

To always install the latest tagged release, regardless of which one that is:

remotes::install_github("alexdray86/ClimbTheCliff@*release", force = TRUE)