parati
This is the released version of parati; for the devel version, see parati.
Parental Allele Transmission Inference for Trio Genotype Data
Bioconductor version: Release (3.23)
Infers maternal and paternal transmitted and non-transmitted alleles from phased trio genotype data. The package supports SNP-level analyses of genetic nurture and transgenerational effects. It interoperates with Bioconductor VCF infrastructure through support for VariantAnnotation::VCF objects and returns R objects for downstream analysis.
Author: Jinyi Che [aut, cre]
Maintainer: Jinyi Che <chejinyi777 at gmail.com>
citation("parati")):
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("parati")
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("parati")| parati Workflow | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Genetics, SNP, Sequencing, Software, VariantAnnotation |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | GPL-3 + file LICENSE |
| Depends | |
| Imports | data.table, methods, openxlsx, R.utils, vcfR, VariantAnnotation, SummarizedExperiment, BiocGenerics, GenomeInfoDb |
| System Requirements | |
| URL | https://github.com/newche/parati |
| Bug Reports | https://github.com/newche/parati/issues |
See More
| Suggests | BiocStyle, knitr, optparse, rmarkdown, testthat (>= 3.0.0), waldo |
| 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 | parati_1.0.0.tar.gz |
| Windows Binary (x86_64) | parati_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | parati_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | parati_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/parati |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/parati |
| Bioc Package Browser | https://code.bioconductor.org/browse/parati/ |
| Package Short Url | https://bioconductor.org/packages/parati/ |
| Package Downloads Report | Download Stats |