Provides a set of tools to perform quantitative
    trait locus (QTL) analysis in experimental crosses. It is a
    reimplementation of the 'R/qtl' package to better handle
    high-dimensional data and complex cross designs.
    Broman et al. (2019) <doi:10.1534/genetics.118.301595>.

Functions to convert data structures among the 'qtl2', 'qtl', and 'DOQTL' packages for mapping quantitative trait loci (QTL).

Uses the 'fst' package to store genotype probabilities on disk for the 'qtl2' package. These genotype probabilities are a central data object for mapping quantitative trait loci (QTL), but they can be quite large. The facilities in this package enable the genotype probabilities to be stored on disk, leading to reduced memory usage with only a modest increase in computation time.

Functions to plot QTL (quantitative trait loci) analysis
    results and related diagnostics.
    Part of 'qtl2', an upgrade of the 'qtl'
    package to better handle high-dimensional data and complex cross
    designs.

Routines in 'qtl2' to study allele patterns in quantitative trait loci (QTL)
    mapping over a chromosome.
    Useful in crosses with more than two alleles to identify how sets of alleles,
    genetically different strands at the same locus, have different response levels.
    Plots show profiles over a chromosome.
    Can handle multiple traits together.
    See <https://github.com/byandell/qtl2pattern>.

We implement an
    adaptation of Jiang & Zeng's (1995) <doi:10.1093/genetics/140.3.1111> likelihood ratio test for testing
    the null hypothesis of pleiotropy against the alternative hypothesis,
    two separate quantitative trait loci. The test differs from that in Jiang & Zeng (1995)
    and that in Tian et al. (2016) <doi:10.1534/genetics.115.183624> in
    that our test accommodates multiparental populations.

Datasets for the book, A Guide to QTL Mapping with R/qtl.
    Broman and Sen (2009) <doi:10.1007/978-0-387-92125-9>.

Densitometric evaluation of the photo-archived quantitative thin-layer chromatography (TLC) plates.