Available software:
[ R/qtl |
R/broman |
R/xoi |
R/lineup |
R/ricalc |
R/negenes |
R/npem |
R/fingers |
R/geesibsor |
R/qtlsim |
RelCheck |
f2 ]
Also see my github page. The R packages below are available through CRAN or github.
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.
A package, composed of tools for analyzing QTL experiments, for use with R (aka Gnu S), an open-source implementation of the S language.
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
Various R functions that I find useful.
Software for the analysis of crossover interference in experimental crosses, particularly regarding the gamma model.
Software for detecting and correcting sample mix-ups between two sets of measurements, such as between gene expression data on two tissues.
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)]
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.
Software for analyzing cell proliferation assays using the normal-Poisson mixture model described by Broman et al. (J Immunol Meth 198:119-132, 1996).
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.
Software for estimating the odds ratio for siblings for a binary phenotype, adjusting for covariates, using generalized estimating equations.
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.
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: I am no longer actively developing this software. 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 use the software, please reference the above papers in any publications.
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 0.50 (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, and I'm no longer actively developing this software. Look at R/qtl, instead.
| Last modified: Fri May 18 07:57:11 2012 |