The Robust Ancestry Inference using Data Synthesis (RAIDS) package enables accurate and robust inference of genetic ancestry from various types of molecular data, including whole-genome, whole-exome, targeted gene panels and RNA sequences, as described in our manuscript. Our tools retain high accuracy in presence of somatic alterations, such as those caused by cancer.
This code and analysis pipeline were designed and developed for the following publication:
Pascal Belleau, Astrid Deschênes, Nyasha Chambwe, David A. Tuveson, Alexander Krasnitz; Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58. https://doi.org/10.1158/0008-5472.CAN-22-0682
Pascal Belleau, Astrid Deschênes, David A. Tuveson and Alexander Krasnitz
If you use the RAIDS package for a publication, we would ask you to cite the following:
Pascal Belleau, Astrid Deschênes, Nyasha Chambwe, David A. Tuveson, Alexander Krasnitz; Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58. https://doi.org/10.1158/0008-5472.CAN-22-0682
If you follow the protocol from Cancer Bioinformatics, you can cite the following:
Belleau, P., Deschênes, A., Tuveson, D.A., Krasnitz, A. (2025). Inference of Genetic Ancestry from Cancer-Derived Molecular Data with RAIDS. In: Krasnitz, A., Belleau, P. (eds) Cancer Bioinformatics. Methods in Molecular Biology, vol 2932. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-4566-6_8
The RAIDS package is now an official package of Bioconductor.
The current Bioconductor release can be directly downloaded from their website: Current release
To install this package from Bioconductor, start R (version "4.3" or later) and enter:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RAIDS")
To install the latest version accessible from Github, the devtools package is required.
## Load required package
library(devtools)
## Install the latest version of RAIDS
devtools::install_github('KrasnitzLab/RAIDS')
This package and the underlying RAIDS code are distributed under the Apache-2.0 license. You are free to use and redistribute this software.
For more information on Apache-2.0 License see https://opensource.org/licenses/Apache-2.0
Please contact us for bug fixes or with feature requests.
Thanks!