Package: dcifer 1.3.0

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_1.3.0.tar.gz
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dcifer_1.3.0.tgz(r-4.4-x86_64)dcifer_1.3.0.tgz(r-4.4-arm64)dcifer_1.3.0.tgz(r-4.3-x86_64)dcifer_1.3.0.tgz(r-4.3-arm64)
dcifer_1.3.0.tar.gz(r-4.5-noble)dcifer_1.3.0.tar.gz(r-4.4-noble)
dcifer_1.3.0.tgz(r-4.4-emscripten)dcifer_1.3.0.tgz(r-4.3-emscripten)
dcifer.pdf |dcifer.html✨
dcifer/json (API)
NEWS

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

Peer review:

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

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

Datasets:

On CRAN:

4.88 score 5 stars 15 scripts 214 downloads 15 exports 0 dependencies

Last updated 8 months agofrom:ac888d189c. Checks:OK: 9. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 01 2024
R-4.5-win-x86_64OKDec 01 2024
R-4.5-linux-x86_64OKDec 01 2024
R-4.4-win-x86_64OKDec 01 2024
R-4.4-mac-x86_64OKDec 01 2024
R-4.4-mac-aarch64OKDec 01 2024
R-4.3-win-x86_64OKDec 01 2024
R-4.3-mac-x86_64OKDec 01 2024
R-4.3-mac-aarch64OKDec 01 2024

Exports:calcAfreqformatAfreqformatDatgenerateRevalgetCOIibdDatibdEstMibdPairlogRevalmatchAfreqplotColorbarplotRelprobUxUyreadAfreqreadDat

Dependencies:

Dcifer: Genetic Distance Between Polyclonal Infections

Rendered fromvignetteDcifer.Rmdusingknitr::rmarkdownon Dec 01 2024.

Last update: 2023-12-11
Started: 2022-06-05