XSim.jl

Documentation for XSim.jl

Features

• Efficient CPOS algorithm
• Founders characterized by real genome sequence data
• Complicated pedigree structures among descendants
• Strong extensibilty
• Modularism design
• Straightforward interface

Installation

julia> using Pkg
julia> Pkg.add("XSim")

or the beta version

julia> Pkg.add(PackageSpec(name="XSim", rev="master"))

Outline

Home

• XSim.jl
• • Features
  • Installation
  • Outline
  • Cite XSimV2

Demo

• Demo: Step by Step
• • Step 0. Load XSim
  • Step 1. Setup Genome and Phenome
  • Step 2. Initialize Founders
  • Step 3. Mating
  • Step 4. Selection
  • Step 5. Expand to Multiple Generations
  • Complete Codes

Core Functions

• Build Genome
• • Quick Start
  • Build by a File or a DataFrame
  • Build by Pre-Loaded Genome
  • Build by Explicit Definition

• Build Phenome
• • Quick Start
  • Build by a File or a DataFrame
  • Build by QTL Effects

• Cohort and Founders
• • Initialize by Population Size
  • Initialize by Genotypes/Haplotypes Files
  • Properties

• Mating
• • Arguments
  • Outputs
  • Examples

• Selection
• • Arguments
  • Outputs
  • Examples

• Genetic Evaluation (JWAS)
• • Arguments
  • Outputs
  • Example of the phenotypes Dataframe
  • Examples
  • References

• Breed: Wrap-up Function
• • Arguments
  • Outputs
  • Examples

Case Studies

• Rotational Cross-Breeding
• • References

• Nested Association Mapping
• • References

Library

• Library
• • Index
  • Contents

Cite XSimV2

BibTex

@article{chen_xsim_2022,
 title = {XSim version 2: simulation of modern breeding programs},
 volume = {12},
 issn = {2160-1836},
 url = {<https://doi.org/10.1093/g3journal/jkac032>},
 doi = {10.1093/g3journal/jkac032},
 number = {4},
 urldate = {2022-05-26},
 journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
 author = {Chen, Chunpeng James and Garrick, Dorian and Fernando, Rohan and Karaman, Emre and Stricker, Chris and Keehan, Michael and Cheng, Hao},
 month = apr,
 year = {2022},
}

Bibliography

Chen, C.J., D. Garrick, R. Fernando, E. Karaman, C. Stricker, M. Keehan, and H. Cheng. 2022. XSim version 2: simulation of modern breeding programs. G3 Genes|Genomes|Genetics 12:jkac032. doi:10.1093/g3journal/jkac032.