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RAIDS

Accurate Inference of Genetic Ancestry from Cancer Sequences


Bioconductor version: Release (3.18)

This package implements specialized algorithms that enable genetic ancestry inference from various cancer sequences sources (RNA, Exome and Whole-Genome sequences). This package also implements a simulation algorithm that generates synthetic cancer-derived data. This code and analysis pipeline was designed and developed for the following publication: Belleau, P et al. Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.

Author: Pascal Belleau [cre, aut] , Astrid Deschênes [aut] , David A. Tuveson [aut] , Alexander Krasnitz [aut]

Maintainer: Pascal Belleau <pascal_belleau at hotmail.com>

Citation (from within R, enter citation("RAIDS")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RAIDS")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RAIDS")
Accurate Inference of Genetic Ancestry from Cancer-derived Sequences HTML R Script
Population reference dataset GDS files HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DimensionReduction, GeneticVariability, Genetics, PrincipalComponent, Sequencing, Software, WholeGenome
Version 1.0.0
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License Apache License (>= 2)
Depends R (>= 4.2.0), gdsfmt, SNPRelate, stats, utils, GENESIS
Imports S4Vectors, GenomicRanges, ensembldb, BSgenome, AnnotationDbi, methods, class, pROC, IRanges, AnnotationFilter, rlang, VariantAnnotation, MatrixGenerics
System Requirements
URL https://krasnitzlab.github.io/RAIDS/
Bug Reports https://github.com/KrasnitzLab/RAIDS/issues
See More
Suggests testthat, knitr, rmarkdown, BiocStyle, withr, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86
Linking To
Enhances
Depends On Me
Imports Me
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package RAIDS_1.0.0.tar.gz
Windows Binary RAIDS_1.0.0.zip
macOS Binary (x86_64) RAIDS_1.0.0.tgz
macOS Binary (arm64) RAIDS_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RAIDS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RAIDS
Bioc Package Browser https://code.bioconductor.org/browse/RAIDS/
Package Short Url https://bioconductor.org/packages/RAIDS/
Package Downloads Report Download Stats