genotypeeval

DOI: 10.18129/B9.bioc.genotypeeval  

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.17 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see genotypeeval.

QA/QC of a gVCF or VCF file

Bioconductor version: 3.17

Takes in a gVCF or VCF and reports metrics to assess quality of calls.

Author: Jennifer Tom [aut, cre]

Maintainer: Jennifer Tom <tom.jennifer at gene.com>

Citation (from within R, enter citation("genotypeeval")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("genotypeeval")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews BatchEffect, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation
Version 1.31.1
In Bioconductor since BioC 3.2 (R-3.2) (8 years)
License file LICENSE
Depends R (>= 3.4.0), VariantAnnotation
Imports ggplot2, rtracklayer, BiocGenerics, GenomicRanges, GenomeInfoDb, IRanges, methods, BiocParallel, graphics, stats
LinkingTo
Suggests rmarkdown, testthat, SNPlocs.Hsapiens.dbSNP141.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64) genotypeeval_1.31.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/genotypeeval
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/genotypeeval
Package Short Url https://bioconductor.org/packages/genotypeeval/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: