## software

#### R/qtl

An R package with tools for analyzing QTL experiments.

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

#### R/qtl2

A reimplementation of R/qtl, to better handle high-dimensional data and complex cross designs (such as the Collaborative Cross, MAGIC, heterogeneous stock, and Diversity Outbred mice).

To receive announcements about updates to R/qtl2 (and R/qtl1), join the Google group, R/qtl announcements.

To participate in discussion about the use of R/qtl2, join the Google group, R/qtl2 discussion

#### R/qtlcharts and d3panels

R/qtlcharts is an R package providing D3-based interactive graphics for QTL experiments.

It is built on the d3panels library (written in CoffeeScript), which provides a set of graphics panels of different types (e.g., scatterplot, dotchart, and heatmap).

#### R/broman

Various R functions that I find useful, assembled into an R package.

#### aRxiv

R package for searching arXiv (an archive of electronic preprints for computer science, mathematics, physics, quantitative biology, quantitative finance, and statistics). The package is part of the rOpenSci project.

#### R/lineup and R/lineup2

R packages for detecting and correcting sample mix-ups between two sets of measurements, such as between gene expression data on two tissues. R/lineup is closely tied to the R/qtl package. R/lineup2 is a redesign to be more general.

#### R/simcross

An R package for simulating general experimental crosses (such as advanced intercross lines and the diversity outcross), for use with R/qtl.

#### R/xoi

An R package for the analysis of crossover interference in experimental crosses, particularly regarding the gamma model.

#### R/mbmixture

An R package for evaluating whether a microbiome sample is the mixture of
two source samples. We are thinking of shotgun sequencing data on the
microbiome sample plus dense SNP genotype data on the two potential
source samples. We assume that the data has been reduced to a
three-dimensional array of read counts: the 3 possible SNP genotypes
for the first sample × the 3 possible SNP genotypes of the
second sample × the 2 possible SNP alleles on the reads. We then
fit a model with contaminant probability *p* = proportion of the
microbiome sample coming from the second sample and *e* = rate of sequencing
errors. See the related paper:
Lobo et al. (2021)
Identification of sample mix-ups and mixtures in microbiome data in
Diversity Outbred mice. G3
(Bethesda) 11:jkab308

#### R/mmconvert

An R package for converting mouse genome positions between genetic and physical maps. This is a re-implementation of the basic functionality of the mouse map converter web service from Gary Churchill’s group at the Jackson Lab. See also the Cox genetic map V3, updated for the mouse genome genome build 39 coordinates, and our annotation files for the MUGA arrays.

#### R/GNapi

An R package to interface with the GeneNetwork API.

#### D3 examples

Various examples of D3-based interactive graphs.

#### R/lmmlite

An R package for the fit of a simple linear mixed model useful for genome-wide association studies (GWAS) and quantitative trait locus (QTL) mapping.

#### R/negenes

An R package 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.

#### R/ricalc

An R package 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

#### R/npem

An R package for analyzing cell proliferation assays using the normal-Poisson mixture model described by Broman et al. (J Immunol Meth 198:119-132, 1996).

#### R/fingers

An R package 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.

#### R/geesibsor

Software for estimating the odds ratio for siblings for a binary phenotype, adjusting for covariates, using generalized estimating equations.

#### R/qtlsim

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. J Roy Stat Soc B 64:641-656. Also see the R/qtl package.

#### RelCheck

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
Relpair
and
KING.

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.

Sample data [tar.gz | zip] README file: [README.txt] List of updates to the software: [CHANGES.txt]

#### f2

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.

**Note**: 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.