Package: dndscv
Title: Poisson-based dN/dS models to quantify natural selection in
        somatic evolution
Type: Package
Version: 0.0.0.9
Date: 2017-05-11
Author: Inigo Martincorena
Maintainer: Inigo Martincorena <im3@sanger.ac.uk>
Description: This package contains functions for studying selection on coding sequences using a Poisson implementation of dN/dS. A Poisson model of dN/dS facilitates the study of selection beyond traditional codon models, including complex context-dependent mutation effects and selection on nonsense and splice site mutations. This model is best suited for resequencing studies, with very low density of mutations per base pair. The model was initially developed for cancer genome sequencing studies, and specific functions are provided to perform driver gene discovery using the dNdScv method on human cancer genomic data. The first beta version of this package only supports analyses of human data. Future versions of the package will support analyses on any species using a general FASTA input format.
Reference: Martincorena I et al, 2017. Universal patterns of selection
        in cancer and somatic tissues. BioRxiv.
        https://doi.org/10.1101/132324
Imports: seqinr, Biostrings, MASS, GenomicRanges
LazyData: false
License: GPL-3
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
RoxygenNote: 6.0.1
Built: R 4.4.3; ; 2025-05-08 11:05:34 UTC; unix
