Package: dcifer 1.5.2

Inna Gerlovina

dcifer: Genetic Relatedness Between Polyclonal Infections

An implementation of Dcifer (Distance for complex infections: fast estimation of relatedness), an identity by descent (IBD) based method to calculate genetic relatedness between polyclonal infections from biallelic and multiallelic data. The package includes functions that format and preprocess the data, implement the method, and visualize the results. Gerlovina et al. (2022) <doi:10.1093/genetics/iyac126>.

Authors:Inna Gerlovina [aut, cre]

dcifer_1.5.2.tar.gz
dcifer_1.5.2.zip(r-4.7)dcifer_1.5.2.zip(r-4.6)dcifer_1.5.2.zip(r-4.5)
dcifer_1.5.2.tgz(r-4.6-x86_64)dcifer_1.5.2.tgz(r-4.6-arm64)dcifer_1.5.2.tgz(r-4.5-x86_64)dcifer_1.5.2.tgz(r-4.5-arm64)
dcifer_1.5.2.tar.gz(r-4.7-arm64)dcifer_1.5.2.tar.gz(r-4.7-x86_64)dcifer_1.5.2.tar.gz(r-4.6-arm64)dcifer_1.5.2.tar.gz(r-4.6-x86_64)
dcifer_1.5.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
dcifer/json (API)
NEWS

# Install 'dcifer' in R:
install.packages('dcifer', repos = c('https://plasmogenepi.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/eppicenter/dcifer/issues

Pkgdown/docs site:https://eppicenter.github.io

Datasets:

On CRAN:

Conda:

5.85 score 8 stars 25 scripts 303 downloads 16 exports 0 dependencies

Last updated from:b6255509bb. Checks:13 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK133
linux-devel-x86_64OK115
source / vignettesOK139
linux-release-arm64OK128
linux-release-x86_64OK112
macos-release-arm64OK113
macos-release-x86_64OK204
macos-oldrel-arm64OK90
macos-oldrel-x86_64OK217
windows-develOK108
windows-releaseOK97
windows-oldrelOK103
wasm-releaseOK98

Exports:calcAfreqformatAfreqformatDatgenerateRevalgetCOIibdDatibdEstMibdPairlogRevalmatchAfreqmixMatplotColorbarplotRelprobUxUyreadAfreqreadDat

Dependencies:

Dcifer: Genetic Distance Between Polyclonal Infections

Rendered fromvignetteDcifer.Rmdusingknitr::rmarkdownon Jun 05 2026.

Last update: 2025-11-07
Started: 2022-06-05