genotypeeval
This package is for version 3.9 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: 3.9
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 "3.6") 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 | |
| NEWS | Text |
| LICENSE | Text |
Details
| biocViews | BatchEffect, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (8.5 years) |
| License | file LICENSE |
| Depends | R (>= 3.4.0), VariantAnnotation |
| Imports | ggplot2, rtracklayer, BiocGenerics, GenomicRanges, GenomeInfoDb, IRanges, methods, BiocParallel, 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 | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | genotypeeval_1.16.0.tar.gz |
| Windows Binary | genotypeeval_1.16.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | genotypeeval_1.16.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/genotypeeval |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/genotypeeval |
| Bioc Package Browser | https://code.bioconductor.org/browse/genotypeeval/ |
| Package Short Url | https://bioconductor.org/packages/genotypeeval/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |