CLIMB — bulk deconvolution into cell-type abundance and cell-type expression

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, posted under an earlier title — will be updated on publication).

Source code: github.com/alexdray86/ClimbTheCliff

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