RAIDS
This is the released version of RAIDS; for the devel version, see RAIDS.
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]
, Astrid Deschênes [aut]
, David A. Tuveson [aut]
, Alexander Krasnitz [aut]
Maintainer: Pascal Belleau <pascal_belleau at hotmail.com>
citation("RAIDS")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text |
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 |
See More
| 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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/RAIDS/ |
| Package Short Url | https://bioconductor.org/packages/RAIDS/ |
| Package Downloads Report | Download Stats |