GDSAnnotator
This is the development version of GDSAnnotator; to use it, please install the devel version of Bioconductor.
Whole-genome variant annotation data manipulation using GDS files
Bioconductor version: Development (3.24)
Fast and memory-efficient manipulation of whole-genome variant annotation data stored in Genomic Data Structure (GDS) files. The annotated GDS (aGDS) format introduced by FAVOR stores the FAVOR annotations of the variants together with the genotypes in one SeqArray GDS file. This package generalizes the format to annotation GDS files of any source, with or without genotypes. Annotation resources and annotator outputs, including FAVOR, gnomAD, Ensembl VEP and SnpEff, are converted into compact SeqArray-compatible GDS files with random access. Variants can be given as chr-pos-ref-alt strings, data frames, GRanges objects, VCF files or objects, or SeqArray GDS files. They are annotated by querying the annotation files, and the annotations can be written back into a genotype GDS file. Summary statistics of the variants and their annotations are computed in a single pass over a file and rendered as a VEP/SnpEff-like report. The package is intended for large-scale whole-genome sequencing studies.
Author: Xiuwen Zheng [aut, cre]
, Yuantao (Raven) Chen [ctb], Hufeng Zhou [ctb]
Maintainer: Xiuwen Zheng <xiuwen.zheng at abbvie.com>
citation("GDSAnnotator")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("GDSAnnotator")
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("GDSAnnotator")| GDSAnnotator: Whole-genome variant annotation | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, DataImport, DataRepresentation, Genetics, GenomeAnnotation, GenomicVariation, Infrastructure, Sequencing, Software, VariantAnnotation, WholeGenome |
| Version | 0.99.2 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL-3 |
| Depends | R (>= 4.6.0), gdsfmt(>= 1.32.0), SeqArray(>= 1.53.2) |
| Imports | methods, utils, IRanges, GenomicRanges, S4Vectors |
| System Requirements | |
| URL | https://github.com/zhengxwen/GDSAnnotator |
| Bug Reports | https://github.com/zhengxwen/GDSAnnotator/issues |
See More
| Suggests | VariantAnnotation, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) |
| 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 | GDSAnnotator_0.99.2.tar.gz |
| Windows Binary (x86_64) | GDSAnnotator_0.99.2.zip |
| macOS Binary (big-sur-x86_64) | GDSAnnotator_0.99.2.tgz |
| macOS Binary (sonoma-arm64) | GDSAnnotator_0.99.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GDSAnnotator |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GDSAnnotator |
| Bioc Package Browser | https://code.bioconductor.org/browse/GDSAnnotator/ |
| Package Short Url | https://bioconductor.org/packages/GDSAnnotator/ |
| Package Downloads Report | Download Stats |