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R/qtl: A QTL mapping environment
R package developed by S. Bihorel ([email protected]) as a user-friendly toolkit for modeling and simulation in the field of pharmacometrics. ScaRabee allows the simulation and optimization of models defined with closed form solutions, ordinary or delay differential equations using the R language (R = 2.11). ScaRabee is an open-source. Download R for Mac OS X for Mac to gNU S statistical computing and graphics. R for Mac OS X has had 1 update within the past 6 months. R is a computer language. It’s a tool for doing the computation and number-crunching that set the stage for statistical analysis and decision-making. RStudio is an open source integrated development environment (IDE) for creating and running R code. It’s available in versions for Windows, Mac, and Linux. Although you don’t need an IDE in order.
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- R is widely used for statistical software development and data analysis, and has become a de-facto standard among statisticians for the development of statistical software. R's source code is freely available under the GNU General Public License, and pre-compiled binary versions are provided for Microsoft Windows, Mac OS X, and several Linux.
Software for mapping quantitative trait loci inexperimental crosses
Current version: 1.46-2 (2020-02-28)
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Try theR/qtlcharts package:interactive graphics for QTL data.
Check out our book:A Guide to QTL Mapping with R/qtl, by Karl W. Broman andŚaunak Sen.
About R/qtl | About R |
R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses. It is implemented as an add-on package for the freely available and widely used statistical language/software R (see the R project homepage). The development of this software as an add-on to R allows us 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. Our 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. We have implemented the main HMM algorithms, with allowance for the presence of genotyping errors, for backcrosses, intercrosses, and phase-known four-way crosses. 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 and Haley-Knott regression. R/qtl is distributed as source code for unix or compiled code for Windows or Mac. R/qtl is released under the GNU General Public License. To download the software, you must agree to the terms in that download. | R is an open-source implementation of the S language. As described onthe R projecthomepage: 'R is a system for statistical computation andgraphics. It consists of a language plus a run-time environment withgraphics, a debugger, access to certain system functions, and theability to run programs stored in script files. 'The core of R is an interpreted computer languagewhich allows branching and looping as well as modular programmingusing functions. Most of the user-visible functions in R are writtenin R. It is possible for the user to interface to procedures writtenin the C, C++, or FORTRAN languages for efficiency. The R distributioncontains functionality for a large number of statisticalprocedures. Among these are: linear and generalized linear models,nonlinear regression models, time series analysis, classicalparametric and nonparametric tests, clustering and smoothing. There isalso a large set of functions which provide a flexible graphicalenvironment for creating various kinds of datapresentations. Additional modules are available for a variety ofspecific purposes.' R is freely available for Windows, unix and MacOS, and may be downloaded from the Comprehensive R Archive Network (CRAN). Learning R may require a formidable investment of time, but it will definitely be worth the effort. Numerous free documents on getting started with R are available on CRAN. In addition, several books are available on R, S and S-PLUS; for example, see WN Venables, BD Ripley (2002) Modern Applied Statistics with S (4thed, Springer) or P Dalgaard (2008) Introductory statistics with R (2nd ed, Springer). See my Introduction to R page for further links. |
Contact forproblems/questions/suggestions: Karl W Broman
Authors: Karl W Broman and Hao Wu, with ideas from Gary Churchill and Śaunak Sen and contributions from Danny Arends, Timothée Flutre, Ritsert Jansen, Pjotr Prins, Lars Rönnegård, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, and Brian Yandell
Google Groups: We've created two GoogleGroups for email announcements regarding software updates (R/qtl announcements)and for discussion about the use of the software (R/qtl discussion). Note that youshould join just one of these two groups; all announcements will alsobe sent to the discussion group.
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Other QTL mapping software
MapMaker/QTL | GeneNetwork |
QTL Cartographer | MultiQTL |
R/qtlDesign | The QTL Cafe |
HAPPY | Kajsa Ljungberg's software |
MapQTL | QTLMap |
Multimapper |
Free Statistical Software Download
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