Available software: [ R/qtl | RelCheck | R/ricalc | R/negenes | R/npem | R/fingers | R/geesibsor | R/qtlsim | f2 ]
All of the software is licensed under the GNU General Public License. Download and use of this software implies agreement to the terms in that license.
Version 1.14-2 (30 Sep 2009)
A package, composed of tools for analyzing QTL experiments, for use with R (aka Gnu S), an open-source implementation of the S language. This is written in collaboration with Gary Churchill (at the Jackson Laboratory) and others.
Note: See also Gary Churchill and Saunak Sen's pseudomarker programs (in Matlab).
The ReadMe file gives some installation instructions.
To receive announcements about updates to R/qtl, join the
Google group, R/qtl announcements.
To participate in discussion about the use of R/qtl, join the
Google group, R/qtl discussion
Version 0.67 (24 August 2000)
Software for verifying relationships between all pairs of individuals in a linkage study, using the approach of Boehnke and Cox (Am J Hum Genet, 61:423-429, 1997), with the modification described by Broman and Weber (Am J Hum Genet 63:1563-1564, 1998), to allow for the presence of genotyping errors. We look only at the relationships MZ twins, parent/offspring, fullsibs, halfsibs and unrelated.
Note: You may wish to check out Mary Sara McPeek and Lei Sun's program PREST. It has a similar aim, and calculates a more extensive set of statistics, includes measures of statistical significance, and also looks at avuncular and first cousin relationships. Other alternatives include the programs Borel, Relpair, Relative, Reltype and Siberror. Go to the Rockefeller software list to find these programs.
The input/output for my program is rather crude. If you have any suggestions for improvements, please send me an email. If you use the software, please reference the above papers in any publications, and please let me know whether or not you find it valuable.
A perl script for converting data from linkage format to that used by relcheck is included with the software.
README file: [README.txt]
List of updates to the software: [CHANGES.txt]
To receive announcements about updates to Relcheck, join the Google group, Relcheck announcements.
Version 0.52-1 (9 October 2007)
Software for calculation of two- and three-locus probabilities in multiple-strain recombinant inbred lines, and the simulation of such lines. See the related paper: Broman KW (2005) The genomes of recombinant inbred lines. Genetics 169:1133-1146 [PubMed | pdf (525k)]
The software is bundled as a package for R (aka Gnu S), an open-source implementation of the S language.
Version 0.98-8 (30 June 2009)
Software for estimating the number of essential genes in a genome on the basis of data from a random transposon mutagenesis experiment. See the related technical report.
The software is bundled as a package for R (aka Gnu S), an open-source implementation of the S language. The package includes data on the numbers of tranposon insertion sites in each gene in the M. tuberculosis CDC1551 genome.
Version 0.50-9 (9 October 2007)
Software for analyzing cell proliferation assays using the normal-Poisson mixture model described by Broman et al. (J Immunol Meth 198:119-132, 1996).
The software is bundled as a package for R (aka Gnu S), an open-source implementation of the S language. But the thing has not been well tested, as so if you are interested in this program, send me an email (kbroman at biostat.wisc.edu) to encourage me to fix up the code.
Version 0.59-7 (9 October 2007)
Software for the inference of full sibling families with data on dominant genetic markers (such as RAPDs), following the hierarchicical clustering approach of Apostol et al. (1993) Theor Appl Genet 86:991-1000. The title follows from Fortran software written by WC Black IV.
The software is bundled as a package for R (aka Gnu S), an open-source implementation of the S language.
Version 0.50-5 (9 October 2007)
Software for estimating the odds ratio for siblings for a binary phenotype, adjusting for covariates, using generalized estimating equations.
The software is bundled as a package for R (aka Gnu S), an open-source implementation of the S language.
Version 0.71-6 (9 October 2007)
Software for testing, by computer simulation, various approaches to mapping QTLs in a backcross experiment. This was written for the manuscript Broman and Speed (2002) A model selection approach for the identication of quantitative trait loci in experimental crosses (with discussion). J Roy Stat Soc B 64:641-656, 731-775. Also see the R/qtl package.
The software is bundled as a package for R (aka Gnu S), an open-source implementation of the S language.
Version 0.50 (7 Feb 2000)
Software for QTL analysis of an F2 intercross experiment, including forward selection for multiple QTLs, all pairs of loci, and pairwise interactions. This is very preliminary. The input and output are not well documented.
| Last modified: Fri Oct 2 00:18:07 2009 |