Package: r-cran-qtl (1.70-1) [debports]

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GNU R package for genetic marker linkage analysis

R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTLs) in experimental crosses. It is implemented as an add-on-package for the freely available and widely used statistical language/software R (see http://www.r-project.org).

The development of this software as an add-on to R allows one to take advantage of the basic mathematical and statistical functions, and powerful graphics capabilities, that are provided with R. Further, the user will benefit by the seamless integration of the QTL mapping software into a general statistical analysis program. The goal is to make complex QTL mapping methods widely accessible and allow users to focus on modeling rather than computing.

A key component of computational methods for QTL mapping is the hidden Markov model (HMM) technology for dealing with missing genotype data. The main HMM algorithms, with allowance for the presence of genotyping errors, for backcrosses, intercrosses, and phase-known four-way crosses were implemented.

The current version of R/qtl includes facilities for estimating genetic maps, identifying genotyping errors, and performing single-QTL genome scans and two-QTL, two-dimensional genome scans, by interval mapping (with the EM algorithm), Haley-Knott regression, and multiple imputation. All of this may be done in the presence of covariates (such as sex, age or treatment). One may also fit higher-order QTL models by multiple imputation.

Other Packages Related to r-cran-qtl

• dep: libblas3

  Basic Linear Algebra Reference implementations, shared library

  or libblas.so.3

  virtual package provided by libatlas3-base, libblas3, libblis4-openmp, libblis4-pthread, libblis4-serial, libopenblas0-openmp, libopenblas0-pthread, libopenblas0-serial

• dep: libc6.1 (>= 2.29)

  GNU C Library: Shared libraries
  also a virtual package provided by libc6.1-udeb

• dep: liblapack3

  Library of linear algebra routines 3 - shared version

  or liblapack.so.3

  virtual package provided by libatlas3-base, liblapack3, libopenblas0-openmp, libopenblas0-pthread, libopenblas0-serial

• dep: r-api-4.0

  virtual package provided by r-base-core

• dep: ruby

  Interpreter of object-oriented scripting language Ruby (default version)

• rec: r-cran-testthat

  GNU R testsuite

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Architecture	Package Size	Installed Size	Files
alpha (unofficial port)	5,403.8 kB	10,369.0 kB	[list of files]