dcifer

Summary sheet

Main use-cases	Genetic relatedness between polyclonal infections
Authors	Inna Gerlovina
Latest version	1.2.0
License	MIT
Website	https://eppicenter.github.io/dcifer/
Code repository	https://github.com/EPPIcenter/dcifer
Publication	https://doi.org/10.1093/genetics/iyac126
Tutorial authors	Shazia Ruybal-Pesántez
Tutorial date	11-Dec-23

Purpose

The dcifer R package is primarily designed to estimate relatedness between polyclonal infections. The data input types must be biallelic or multiallelic data.

The approach uses a likelihood function and statistical inference, and provides these alongside relatedness estimates.

Existing resources

The dcifer R package includes built-in functions for reading and reformatting data, performing preparatory steps, and visualizing the results are also included. This is documented in the dcifer R package website. There is also a tutorial outlining the analysis process using the dcifer R package with microhaplotype data from Mozambique.

Citation

The publication associated with the dcifer R package can be found here (Gerlovina 2022 Genetics).

citation(package = "dcifer")

To cite package 'dcifer' in publications use:

  Gerlovina I (2023). _dcifer: Genetic Relatedness Between Polyclonal
  Infections_. R package version 1.2.1,
  <https://CRAN.R-project.org/package=dcifer>.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {dcifer: Genetic Relatedness Between Polyclonal Infections},
    author = {Inna Gerlovina},
    year = {2023},
    note = {R package version 1.2.1},
    url = {https://CRAN.R-project.org/package=dcifer},
  }