Identification of candidate causal perturbations from differential gene expression data
by Nuno Agostinho nunoagostinho@medicina.ulisboa.pt

cTRAP is an R package designed to compare differential gene expression results with those from known cellular perturbations (such as gene knockdown, overexpression or small molecules) derived from the Connectivity Map (CMap; Subramanian et al., Cell 2017). Such analyses allow not only to infer the molecular causes of the observed difference in gene expression but also to identify small molecules that could drive or revert specific transcriptomic alterations.

Tutorial: cTRAP: identifying candidate causal perturbations from differential gene expression data

de Almeida BP, Saraiva-Agostinho N, Barbosa-Morais NL (2020). cTRAP: Identification of candidate causal perturbations from differential gene expression data. R package version 1.6.0, github.