RAIDS
Accurate Inference of Genetic Ancestry from Cancer Sequences
Bioconductor version: Release (3.20)
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("RAIDS")):
Installation
To install this package, start R (version "4.4") 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 |
| Using wrappper functionss | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiocViews, DimensionReduction, GeneticVariability, Genetics, PrincipalComponent, Sequencing, Software, WholeGenome |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
| 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, ggplot2, stringr |
| 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RAIDS_1.4.0.tar.gz |
| Windows Binary (x86_64) | RAIDS_1.4.0.zip (64-bit only) |
| macOS Binary (x86_64) | RAIDS_1.4.0.tgz |
| macOS Binary (arm64) | RAIDS_1.4.0.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 |