CRAN/E | updog

updog

Flexible Genotyping for Polyploids

Installation

About

Implements empirical Bayes approaches to genotype polyploids from next generation sequencing data while accounting for allele bias, overdispersion, and sequencing error. The main functions are flexdog() and multidog(), which allow the specification of many different genotype distributions. Also provided are functions to simulate genotypes, rgeno(), and read-counts, rflexdog(), as well as functions to calculate oracle genotyping error rates, oracle_mis(), and correlation with the true genotypes, oracle_cor(). These latter two functions are useful for read depth calculations. Run browseVignettes(package = "updog") in R for example usage. See Gerard et al. (2018) doi:10.1534/genetics.118.301468 and Gerard and Ferrao (2020) doi:10.1093/bioinformatics/btz852 for details on the implemented methods.

Citation updog citation info
github.com/dcgerard/updog/
Bug report File report

Key Metrics

Version 2.1.5
R ≥ 3.4.0
Published 2023-11-29 121 days ago
Needs compilation? yes
License GPL-3
CRAN checks updog results

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Maintainer

Maintainer

David Gerard

gerard.1787@gmail.com

Authors

David Gerard

aut / cre

Material

README
NEWS
Reference manual
Package source

Vignettes

Genotyping Many SNPs with multidog()
Oracle Calculations
Simulate Next-Generation Sequencing Data
Example Use of Updog

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

updog archive

Depends

R ≥ 3.4.0

Imports

Rcpp ≥ 0.12.16
RcppArmadillo
assertthat
ggplot2
reshape2
foreach
future
doFuture
doRNG
methods
iterators

Suggests

covr
testthat
SuppDists
knitr
rmarkdown
VariantAnnotation
GenomicRanges
S4Vectors
IRanges

LinkingTo

Rcpp
RcppArmadillo

Reverse Imports

hwep

Reverse Suggests

ldsep
mappoly
polymapR