parati
This is the development version of parati; to use it, please install the devel version of Bioconductor.
Parental Allele Transmission Inference for Trio Genotype Data
Bioconductor version: Development (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")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 |
Details
| biocViews | Genetics, SNP, Sequencing, Software, VariantAnnotation |
| Version | 0.99.7 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| 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_0.99.7.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | parati_0.99.7.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 |