```{image} _static/climb_banner.png
:alt: CLIMB — bulk deconvolution into cell-type abundance and cell-type expression
:width: 100%
```

**ClimbTheCliff** is an R package for deconvolution of bulk RNA-seq data using single-cell RNA-seq references. It provides two complementary methods:

- **CLIMB** — infers cell-type proportions and cell-type-specific gene expression from bulk RNA-seq, using a single-cell reference dataset, without relying on a signature matrix.
- **CLIFF** — takes CLIMB's output together with bulk drug-response data and infers cell-type-specific drug sensitivity, using an Expectation-Maximization algorithm.

Both methods are described in detail in Coudray et al., *Computational deconvolution of drug sensitivity via single-cell–to–bulk transcriptome mapping* (manuscript in revision; [preprint on bioRxiv](https://www.biorxiv.org/content/10.1101/2023.05.10.540140v3), posted under an earlier title — will be updated on publication).

Source code: [github.com/alexdray86/ClimbTheCliff](https://github.com/alexdray86/ClimbTheCliff)

```{toctree}
:maxdepth: 1
:caption: Contents

installation
quickstart
example_data
methods
reference/climb
reference/cliff
```