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Open Source Science

https://github.com/bioconductor-source/raids

https://github.com/bioconductor-source/raids

Science Score: 26.0%

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Repository

Basic Info
  • Host: GitHub
  • Owner: bioconductor-source
  • License: apache-2.0
  • Language: R
  • Default Branch: devel
  • Size: 3.78 MB
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  • Watchers: 2
  • Forks: 0
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Created almost 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme License

README.md

License codecov R-CMD-check-bioc <!-- badges: end -->

Accurate genetic ancestry inference from cancer-derived 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, Astrid Deschênes, David A. Tuveson and 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

Bioconductor Time

The RAIDS package is now an official package of Bioconductor.

The current Bioconductor release can be directly downloaded from their website: Current release

Installation

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')

Documentation

RAIDS Website

RAIDS Get Started

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

Maintainer

Pascal Belleau

Bugs/Feature requests

Please contact us for bug fixes or with feature requests.

Thanks!

Owner

  • Name: (WIP DEV) Bioconductor Packages
  • Login: bioconductor-source
  • Kind: organization
  • Email: maintainer@bioconductor.org

Source code for packages accepted into Bioconductor

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Dependencies

.github/workflows/check-bioc.yaml actions
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/upload-artifact master composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • GENESIS * depends
  • R >= 4.2.0 depends
  • SNPRelate * depends
  • gdsfmt * depends
  • stats * depends
  • utils * depends
  • AnnotationDbi * imports
  • AnnotationFilter * imports
  • BSgenome * imports
  • GenomicRanges * imports
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  • BSgenome.Hsapiens.UCSC.hg38 * suggests
  • BiocStyle * suggests
  • EnsDb.Hsapiens.v86 * suggests
  • GenomeInfoDb * suggests
  • knitr * suggests
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