https://github.com/krasnitzlab/raids
Accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms
https://github.com/krasnitzlab/raids
ancestry cancer-genomics exome-sequencing genomics inference r-language r-package rna-seq rna-sequencing whole-genome-sequencing
Last synced: about 1 year ago
JSON representation
Accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms
- Host: GitHub
- URL: https://github.com/krasnitzlab/raids
- Owner: KrasnitzLab
- License: other
- Created: 2022-04-06T18:47:59.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2025-04-10T00:15:46.000Z (about 1 year ago)
- Last Synced: 2025-04-10T00:28:17.792Z (about 1 year ago)
- Topics: ancestry, cancer-genomics, exome-sequencing, genomics, inference, r-language, r-package, rna-seq, rna-sequencing, whole-genome-sequencing
- Language: R
- Homepage: https://krasnitzlab.github.io/RAIDS/
- Size: 8.13 MB
- Stars: 5
- Watchers: 2
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
Awesome Lists containing this project
README
[](https://opensource.org/licenses/Apache-2.0)
[](https://codecov.io/gh/krasnitzlab/RAIDS)
[](https://github.com/krasnitzlab/RAIDS/actions/workflows/check-bioc.yaml)
# Robust genetic ancestry inference from challenging molecular data with **RAIDS** #
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
## Authors ##
[Pascal Belleau](http://ca.linkedin.com/in/pascalbelleau "Pascal Belleau"),
[Astrid Deschênes](https://www.linkedin.com/in/astriddeschenes "Astrid Deschênes"),
[David A. Tuveson](https://tuvesonlab.labsites.cshl.edu/) and
[Alexander Krasnitz](https://www.cshl.edu/research/faculty-staff/alexander-krasnitz/ "Alexander Krasnitz")
## Citing ##
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
## Bioconductor Package ##
[](https://bioconductor.org/packages/RAIDS)
The **RAIDS** package is now an official package
of [Bioconductor](http://bioconductor.org/).
The current Bioconductor release can be directly downloaded from their website:
[Current release](https://bioconductor.org/packages/RAIDS)
## Installation ##
To install this package
from [Bioconductor](https://bioconductor.org/packages/RAIDS), 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](https://cran.r-project.org/web/packages/devtools/index.html)
package is required.
## Load required package
library(devtools)
## Install the latest version of RAIDS
devtools::install_github('KrasnitzLab/RAIDS')
## Documentation ##
[RAIDS Website](https://krasnitzlab.github.io/RAIDS/)
[RAIDS Get Started](https://krasnitzlab.github.io/RAIDS/articles/RAIDS.html)
## License ##
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](https://opensource.org/licenses/Apache-2.0)
## Maintainer
[Pascal Belleau](https://github.com/belleau/ "Pascal Belleau")
## Bugs/Feature requests ##
[Please contact us](https://github.com/KrasnitzLab/RAIDS/issues) for bug fixes or with feature requests.
Thanks!