RAIDS

This is the released version of RAIDS; for the devel version, see RAIDS.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18

Robust Ancestry Inference using Data Synthesis

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-0802-1071 , Astrid Deschênes [aut] ORCID: 0000-0001-7846-6749 , David A. Tuveson [aut] ORCID: 0000-0002-8017-2712 , Alexander Krasnitz [aut]

Maintainer: Pascal Belleau <pascal_belleau at hotmail.com>

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

Pascal Belleau, Astrid Deschênes, David A. Tuveson, Alexander Krasnitz. RAIDS: Robust Ancestry Inference using Data Synthesis. doi:10.18129/B9.bioc.RAIDS, R package version 1.10.0, https://bioconductor.org/packages/RAIDS.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

Population reference dataset GDS files	HTML	R Script
Robust Ancestry Inference using Data Synthesis	HTML	R Script
Using wrappper functionss	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiocViews, DimensionReduction, GeneticVariability, Genetics, PrincipalComponent, Sequencing, Software, WholeGenome
Version	1.10.0
In Bioconductor since	BioC 3.18 (R-4.3) (3 years)
License	Apache License (>= 2)
Depends	R (>= 4.2.0), gdsfmt, SNPRelate, stats, utils, GENESIS, dplyr, Rsamtools
Imports	S4Vectors, GenomicRanges, ensembldb, BSgenome, AnnotationDbi, methods, class, pROC, IRanges, AnnotationFilter, rlang, VariantAnnotation, MatrixGenerics, ggplot2, stringr
System Requirements
URL	https://krasnitzlab.github.io/RAIDS/
Bug Reports	https://github.com/KrasnitzLab/RAIDS/issues

Suggests	testthat, knitr, rmarkdown, BiocStyle, withr, Seqinfo, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	RAIDS_1.10.0.tar.gz
Windows Binary (x86_64)	RAIDS_1.10.0.zip
macOS Binary (big-sur-x86_64)	RAIDS_1.10.0.tgz
macOS Binary (sonoma-arm64)	RAIDS_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RAIDS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RAIDS
Package Short Url	https://bioconductor.org/packages/RAIDS/
Package Downloads Report	Download Stats