genotypeeval

This package is for version 3.7 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: 3.7

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 "3.5") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("genotypeeval")
genotypeeval_vignette.html HTML
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews BatchEffect, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation
Version 1.12.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License file LICENSE
Depends R (>= 3.3.0), VariantAnnotation
Imports ggplot2, rtracklayer, BiocGenerics, GenomicRanges, GenomeInfoDb, IRanges, methods, BiocParallel, Rtsne, graphics, stats
System Requirements
URL
See More
Suggests rmarkdown, testthat, SNPlocs.Hsapiens.dbSNP141.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report Build Report

Package Archives

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

Source Package genotypeeval_1.12.0.tar.gz
Windows Binary genotypeeval_1.12.0.zip
Mac OS X 10.11 (El Capitan) genotypeeval_1.12.0.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
Old Source Packages for BioC 3.7 Source Archive