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rqtl2_paper.bib
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howpublished = {\url{https://github.com/nickFurlotte/pylmm}},
year = {2015}
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title={Identifying Causal Variants at Loci with Multiple Signals of Association},
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journal={Genetics},
volume={198},
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year={2014}
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title={The {M}ouse {U}niversal {G}enotyping {A}rray: from substrains to subspecies},
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journal={G3},
pages={263--279},
year={2016}
}
@article{MQMpaper,
title={R/qtl: high-throughput multiple {QTL} mapping},
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journal={Bioinformatics},
volume={26},
pages={2990--2992},
year={2010}
}
@article{broman2002,
title={A model selection approach for the identification of quantitative trait loci in experimental crosses},
author={Broman, Karl W and Speed, Terence P},
journal={J R Stat Soc B},
volume={64},
pages={641--656},
year={2002}
}
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title={A model selection approach for the identification of quantitative trait loci in experimental crosses, allowing epistasis},
author={Manichaikul, Ani and Moon, Jee Young and Sen, Saunak and Yandell, Brian S and Broman, Karl W},
journal={Genetics},
volume={181},
pages={1077--1086},
year={2009}
}
@article{gnan2014,
title={The genetic basis of natural variation in seed size and seed number and their trade-off using {A}rabidopsis thaliana {MAGIC} lines},
author={Gnan, S. and Priest, A. and Kover, P. X.},
journal={Genetics},
volume={198},
pages={1751--1758},
year={2014}
}
@article{dekoning2017,
title={Back to the future: multiparent populations provide the key to unlocking the genetic basis of complex traits},
author={de Koning, D. J. and McIntyre, L. M.},
year={2017},
journal = {G3},
volume = {7},
pages = {1617--1618}
}
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title={Genetic dissection of a model complex trait using the {D}rosophila {S}ynthetic {P}opulation {R}esource},
author={King, Elizabeth G and Merkes, Chris M and McNeil, Casey L and Hoofer, Steven R and Sen, Saunak and Broman, Karl W and Long, Anthony D and Macdonald, Stuart J},
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pages={1558--1566},
volume={22},
year={2012}
}
@article{oreper2017,
title={Inbred strain variant database ({ISVDB}): a repository for probabilistically informed sequence differences among the {C}ollaborative {C}ross strains and their founders},
author={Oreper, Daniel and Cai, Yanwei and Tarantino, Lisa M and de Villena, Fernando Pardo-Manuel and Valdar, William},
journal={G3},
volume={7},
pages={1623--1630},
year={2017}
}
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title={Heterogeneous stock populations for analysis of complex traits},
author={Solberg Woods, Leah C and Mott, Richard},
booktitle={Systems Genetics},
pages={31--44},
year={2017},
publisher={Springer}
}
@article{dellacqua2015,
title={Genetic properties of the {MAGIC} maize population: a new platform for high definition QTL mapping in {Z}ea mays},
author={Dell’Acqua, Matteo and Gatti, Daniel M and Pea, Giorgio and Cattonaro, Federica and Coppens, Frederik and Magris, Gabriele and Hlaing, Aye L and Aung, Htay H and Nelissen, Hilde and Baute, Joke and Frascaroli, Elisabetta and Churchill, Gary A. and Inz\'e, Dirk and Morgante, Michele and P\`e, Mario Enrico},
journal={Genome Biol},
volume={16},
pages={167},
year={2015}
}
@article{bandillo2013,
title={Multi-parent advanced generation inter-cross ({MAGIC}) populations in rice: progress and potential for genetics research and breeding.},
author={Bandillo, N and Raghavan, C and Muyco, PA and Sevilla, MA and Lobina, IT and Dilla-Ermita, CJ and Tung, CW and McCouch, S and Thomson, M and Mauleon, R and Singh, Rakesh Kumar and Gregorio, Glenn and Redona, Edilberto and Leung, Hei},
journal={Rice},
volume={6},
pages={11--11},
year={2013}
}
@article{noble2017,
title={Polygenicity and epistasis underlie fitness-proximal traits in the {C}aenorhabditis elegans {M}ultiparental {E}xperimental {E}volution (CeMEE) panel},
author={Noble, Luke M and Chelo, Ivo and Guzella, Thiago and Afonso, Bruno and Riccardi, David D and Ammerman, Patrick and Dayarian, Adel and Carvalho, Sara and Crist, Anna and Pino-Querido, Ania and others},
journal={Genetics},
volume={207},
pages={1663--1685},
year={2017}
}
@article{huang2012,
title={A multiparent advanced generation inter-cross population for genetic analysis in wheat},
author={Huang, Bevan E and George, Andrew W and Forrest, Kerrie L and Kilian, Andrzej and Hayden, Matthew J and Morell, Matthew K and Cavanagh, Colin R},
journal={Plant Biotechnol J},
volume={10},
pages={826--839},
year={2012}
}
@misc{qvalue,
title = {qvalue: Q-value estimation for false discovery rate control},
author = {John D. Storey and Andrew J. Bass and Alan Dabney and David Robinson},
year = {2018},
note = {R package version 2.14.0},
howpublished = {\url{https://github.com/jdstorey/qvalue}}
}
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title={A direct approach to false discovery rates},
author={Storey, John D},
journal={J R Stat Soc B},
volume={64},
pages={479--498},
year={2002}
}
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title={The positive false discovery rate: a {B}ayesian interpretation and the q-value},
author={Storey, John D},
journal={Ann Stat},
volume={31},
pages={2013--2035},
year={2003}
}