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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>.

Version: 1.2.1
Depends: R (≥ 3.5.0)
Imports: stats, utils, graphics
Suggests: knitr, rmarkdown
Published: 2023-12-12
DOI: 10.32614/CRAN.package.dcifer
Author: Inna Gerlovina ORCID iD [aut, cre]
Maintainer: Inna Gerlovina <innager at berkeley.edu>
License: MIT + file LICENSE
URL: https://github.com/EPPIcenter/dcifer, https://eppicenter.github.io/dcifer/
NeedsCompilation: yes
Materials: NEWS
CRAN checks: dcifer results

Documentation:

Reference manual: dcifer.pdf
Vignettes: vignetteDcifer

Downloads:

Package source: dcifer_1.2.1.tar.gz
Windows binaries: r-devel: dcifer_1.2.1.zip, r-release: dcifer_1.2.1.zip, r-oldrel: dcifer_1.2.1.zip
macOS binaries: r-release (arm64): dcifer_1.2.1.tgz, r-oldrel (arm64): dcifer_1.2.1.tgz, r-release (x86_64): dcifer_1.2.1.tgz, r-oldrel (x86_64): dcifer_1.2.1.tgz
Old sources: dcifer archive

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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