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Bioinformatics. 2018 Oct 1;34(19):3380-3381. doi: 10.1093/bioinformatics/bty388.

Palimpsest: an R package for studying mutational and structural variant signatures along clonal evolution in cancer.

Author information

1
INSERM, UMR-1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue Contre le Cancer, Institut Universitaire d'Hématologie; Faculté de Médecine, Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité; Unité de Formation et de Recherche Santé, Médecine, Biologie Humaine, Université Paris 13, Sorbonne Paris Cité, Bobigny, France; Université Paris Diderot, Paris, France.
2
Laboratory for Bioinformatics, Fondation Jean Dausset - CEPH, Paris, France.
3
Assistance Publique-Hôpitaux de Paris, Hopital Europeen Georges Pompidou, Paris, France.

Abstract

Summary:

Cancer genomes are altered by various mutational processes and, like palimpsests, bear the signatures of these different processes. The Palimpsest R package provides a complete workflow for the characterization and visualization of mutational signatures and their evolution along tumor development. The package covers a wide range of functions for extracting both base substitution and structural variant signatures, inferring the clonality of each alteration and analyzing the evolution of mutational processes between early clonal and late subclonal events. Palimpsest also estimates the probability of each mutation being due to each process to predict the mechanisms at the origin of driver events. Palimpsest is an easy-to-use toolset for reconstructing the natural history of a tumor using whole exome or whole genome sequencing data.

Availability and implementation:

Palimpsest is freely available at www.github.com/FunGEST/Palimpsest.

Supplementary information:

Supplementary data are available at Bioinformatics online.

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