# Installation

## Requirements

- R >= 3.5
- [`Biobase`](https://bioconductor.org/packages/Biobase/) — `sc` and `bulk` inputs to `climb()` are `ExpressionSet` objects
- [`glmnet`](https://cran.r-project.org/package=glmnet) — underlying linear/EM model fitting
- [`reshape2`](https://cran.r-project.org/package=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()`:

```r
library(Biobase)
library(glmnet)
library(reshape2)
library(ClimbTheCliff)
```

## From GitHub

Using `devtools`:

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

Using `remotes`:

```r
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`:

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

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

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