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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
fig.align = "center",
out.width = "100%"
)
```
# The **pedsuite**: R packages for pedigree analysis
<!-- badges: start -->
[](https://CRAN.R-project.org/package=pedsuite)
[](https://cran.r-project.org/package=pedsuite)
[](https://cran.r-project.org/package=pedsuite)
<!-- badges: end -->
The **pedsuite** is a collection of R packages for pedigree analysis, covering a variety of applications across several fields. The packages are designed to work harmoniously together, often allowing complex tasks to be solved in a few lines of code.
```{r logos-pedsuite, echo = F}
knitr::include_graphics("man/figures/logos-pedsuite-wheel_1.png")
```
### Core packages
At the centre of the **pedsuite** we find the package **pedtools**, on which all the others depend. In addition, several packages contain basic features often needed in many types of analysis. These are the *core* packages:
* [pedtools](https://github.com/magnusdv/pedtools): Creating and working with pedigrees and marker data
* [forrel](https://github.com/magnusdv/forrel): Forensic pedigree analysis and relatedness analysis
* [pedprobr](https://github.com/magnusdv/pedprobr): Marker probabilities and pedigree likelihoods
* [ribd](https://github.com/magnusdv/ribd): Computation of pedigree-based relatedness coefficients
* [verbalisr](https://github.com/magnusdv/verbalisr): Verbal descriptions of pedigree relationships
### Specialised packages
The following packages are devoted to special applications:
* [ibdsim2](https://github.com/magnusdv/ibdsim2): Simulation of identity-by-descent sharing by family members
* [dvir](https://github.com/magnusdv/dvir): Disaster victim identification
* [paramlink2](https://github.com/magnusdv/paramlink2): Parametric linkage analysis
* [pedbuildr](https://github.com/magnusdv/pedbuildr): Pedigree reconstruction
* [pedFamilias](https://github.com/magnusdv/pedFamilias): Import and export `.fam` files used by the [Familias](https://familias.name/) software
* [pedmut](https://github.com/magnusdv/pedmut): Mutation models for pedigree likelihood computations
* [segregatr](https://github.com/magnusdv/segregatr): Segregation analysis for clinical variant interpretation
### Retired packages
These packages have been superseded by other packages and are no longer compatible with the rest of the **pedsuite**. They are maintained only for legacy purposes and should not be used in new projects.
* [paramlink](https://CRAN.R-project.org/package=paramlink): This package marked the birth of the **pedsuite**. Originally intended for parametric linkage analysis, it also contained the seeds of the current packages **pedtools**, **pedprobr**, **ribd** and **forrel**.
* [IBDsim](https://CRAN.R-project.org/package=IBDsim): This is replaced by **ibdsim2**. (Regrettably, the name 'IBDsim' is very similar to that of the unrelated (non-R) software 'IBDSim' ([Leblois, Estoup & Rousset](https://www1.montpellier.inrae.fr/CBGP/software/ibdsim/index.html)).)
### Imported packages
* [kinship2](https://CRAN.R-project.org/package=kinship2): Pedigree plotting in the **pedsuite** depends on **kinship2** ([Sinnwell, Therneau & Schaid](https://doi.org/10.1159/000363105)) for pedigree alignment calculations.
## Shiny apps
Several Shiny apps based on the **pedsuite** have been developed. Read more about them here:
* [QuickPed](https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html): Interactive pedigree builder and relatedness analyser
* [DIVIANA](https://magnusdv.github.io/pedsuite/articles/web_only/diviana.html):
Disaster victim identification
* [ibdsim2-shiny](https://magnusdv.github.io/pedsuite/articles/web_only/ibdsim2-shiny.html): IBD distributions in pedigrees
* [KLINK](https://magnusdv.github.io/pedsuite/articles/web_only/klink.html): Kinship analysis with linked markers
* [LinkageLab](https://magnusdv.github.io/pedsuite/articles/web_only/linkagelab.html): Playing with linked markers
* [ibdClassifier](https://magnusdv.github.io/pedsuite/articles/web_only/ibdClassifier.html): Classifying relationships based on IBD segments