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R/qtl software for mapping quantitative trait lociR/qtl software for mapping quantitative trait loci (QTL) in experimental crosses.
http://www.rqtl.org/
R/qtl software for mapping quantitative trait loci (QTL) in experimental crosses.
http://www.rqtl.org/
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R/qtl software for mapping quantitative trait loci | rqtl.org Reviews
https://rqtl.org
R/qtl software for mapping quantitative trait loci (QTL) in experimental crosses.
rqtl.org
A Guide to QTL Mapping with R/qtl: Complements
http://www.rqtl.org/book
A Guide to QTL Mapping with R/qtl: Online complements. This page contains online complements to A Guide to QTL Mapping with R/qtl. By Karl W. Broman. And Śaunak Sen. Buy a copy (ISBN: 978-0-387-92124-2):. Directly from the publisher, Springer. Our aim in this book is to give an overview of the practical aspects of the analysis of QTL mapping experiments based on inbred line crosses, with explicit instructions on the use of the R/qtl software. An add-on package for R. Vol 32, Book Review 5 [ pdf (133k).
Sample graphics from R/qtl
http://www.rqtl.org/graphs
Sample graphics from R/qtl. Summary plot for an experimental cross. The top left panel displays the pattern of missing genotype data; the top right shows the genetic map. The lower panels are histograms of two phenotypes. Pattern of missing genotype data in a cross. Black pixels indicate missing genotypes. Gray pixels indicate partially missing genotypes (in an intercross, genotypes coded as "not B" or "not A"). Locations of markers on a genetic map. Side-by-side comparison of two genetic maps. For a sel...
R/qtl Tutorials
http://www.rqtl.org/tutorials
A brief tour of R/qtl: [ pdf. A shorter tour of R/qtl: [ pdf. 19 Oct 2009; slight changes 2 Oct 2011, 21 Mar 2012, and 26 Nov 2012). Users guide for new BC. Tools for R/qtl: [ pdf. Genetic map construction with R/qtl: [ pdf. 4 Nov 2010; slight changes 21 Mar 2012). Tutorial on MQM within R/qtl: [ pdf. 12 May 2010; slight changes 28 Jul 2010 and 13 Oct 2010). New functions for exploring multiple-QTL models: [ pdf. 18 Jul 2008; added color 26 Oct 2010). 27 Oct 2006; added color 26 Oct 2010).
R/qtl FAQ
http://www.rqtl.org/faq
R/qtl Frequently Asked Questions. If you have questions, suggestions, corrections, etc., please email Karl Broman (kbroman at biostat.wisc.edu). I'm having trouble reading my data into R. First, take a look at the help file for the. Function. Next, look at some of the sample data files. It's still not clear to me how X chromosome genotypes should be coded. Are you planning to implement. The list of things we hope to implement in R/qtl is available here. I'm getting the following error/warning; what does ...
Sample data files for R/qtl
http://www.rqtl.org/sampledata
R/qtl sample data files. These files contain sample QTL mapping data in several formats, so that the user may better understand how data may be formatted for import into R via the. Function. These are the same as the. Data set included with the R/qtl package, which may be accessed by typing. The data come from Boyartchuk et al., Nat Genet 27:259-260, 2001.). Please read the help file for. It explains all of the details. With the correct directory (being careful, in Windows, to use either forward slashes (.
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Churchill Group - Software
http://churchill.jax.org/software/pubarray.shtml
Center for Genome Dynamics. Current Version 1.0.0 (April 5th, 2010). PubArray is a desktop application that allows you to turn the analyzed results of your microarray experiment into a web application which is accessible via your browser. Detailed information about PubArray functions can be found on the Help page. Below is a summary of PubArray features:. Imports microarray intensity values and test statistics as exported by J/maanova. Allows for the import of any number of probeset annotation files.
Churchill Group - Software
http://churchill.jax.org/software/jmaanova.shtml
Center for Genome Dynamics. Current Version 1.1.1 (June 7th, 2011). J/maanova is an open sourced desktop application developed by The Churchill Group at The Jackson Laboratory with the aim of simplifying the analysis of microarray experiments. J/maanova allows researchers to access a subset of the functionality available in the R/maanova. The source code for J/maanova can be found at the source code repository. Java 5.0 or greater. All Mac OS X computers come preinstalled with Java). Windows XP (Windows ...
Churchill Group - Disclaimer
http://churchill.jax.org/disclaimer.shtml
Center for Genome Dynamics. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the Software), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:. Data Disclaimer and Fair Use. These data are prov...
Churchill Group - Education & Events
http://churchill.jax.org/events/groupmeeting.shtml
Center for Genome Dynamics. 1:30pm – 2:30pm. Jessica Seavey (Research Administrative Assistant to Gary Churchill - Jessica.Seavey@jax.org.
Churchill Group - News & Publications
http://churchill.jax.org/publications/papers.shtml
Center for Genome Dynamics. Papers - by year. PRDM9 drives evolutionary erosion of hotspots in Mus musculus through haplotype-specific initiation of meiotic recombination. Baker CL, Kajita S, Walker M, Saxl RL, Raghupathy N, Choi K, Petkov PM and Paigen K. PLoS Genetics. 2015;11(1):e1004916. PMCID: PMC4287450 [ Full Text ]. Sensitivity to hepatotoxicity due to epigallocatechin gallate is affected by genetic background in diversity outbred mice. Env Health Persp., 2015;123(3):237-45. [ Full Text ]. Bogue ...
Churchill Group
http://churchill.jax.org/index.shtml
Center for Genome Dynamics. February 3, 2015. Gary Churchill appointed to new computational biology chair [Read More]. November 13, 2014. Teacher in Jackson Laboratory distance-learning program earns NABT Genetics Education Award [Read More]. November 10, 2014. Diversity Outbred Mice better predict human response to chemical exposure [Read More]. Welcome to The Churchill Group. That will improve the power of quantitative trait loci mapping. As well as graphical models. And the Diversity Outbred. Submissi...
Churchill Group - News & Publications
http://churchill.jax.org/publications/publications.shtml
Center for Genome Dynamics. News Relating to the Group and our Research. Talks and posters given by members of our group. Publications from the group. Papers - by year. Manuscripts describing our work organized by year. Papers - by author. Manuscripts describing our work organized by author. Papers - by topic. Manuscripts describing our work organized by topic.
Churchill Group - News & Publications
http://churchill.jax.org/publications/presentations.shtml
Center for Genome Dynamics. Genetic analysis of RNA editing in the Diversity Outbred mice (PDF 0.3 MB). Robert E. Braun, Gary A. Churchill. Gordon Research Conference on RNA Editing, Galveston, TX, Jan 6-11, 2013. Poster. RNA-seq Alignment to Individualized Genomics (PDF 6.5 MB). 40th Maine Biological and Medical Sciences Symposium, Bar Harbor, ME, April 12-13, 2013. Talk. Comparing Diverse Pluripotent Stem Cell Fate Programs Using Cell-Type Specific Data Integration And Machine Learning (PDF 3.6 MB).
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R/qtl software for mapping quantitative trait loci
R/qtl: A QTL mapping environment. Software for mapping quantitative trait loci in experimental crosses. Current version: 1.36-6 (2015-03-05). Try the R/qtlcharts package. Interactive graphics for QTL data. Check out our book:. A Guide to QTL Mapping with R/qtl. By Karl W. Broman and Śaunak Sen. 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 ...
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