swfdrQ.bib

% References for swfdr vignettes


%% Bioconductor package manager
@Manual{biocmanager2018package,
    title = {BiocManager: Access the Bioconductor Project Package Repository},
    author = {Martin Morgan},
    year = {2018},
    note = {R package version 1.30.4},
    url = {https://CRAN.R-project.org/package=BiocManager},
  }


%% Definitions of pi0 and q
@article{storey2002direct,
  title={A direct approach to false discovery rates},
  author={Storey, John D},
  journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume={64},
  number={3},
  pages={479--498},
  year={2002},
  publisher={Wiley Online Library}
}
@article{storey2003statistical,
  title={Statistical significance for genomewide studies},
  author={Storey, John D and Tibshirani, Robert},
  journal={Proceedings of the National Academy of Sciences},
  volume={100},
  number={16},
  pages={9440--9445},
  year={2003},
  publisher={National Acad Sciences}
}
@Manual{qvalue2018package,
  title = {qvalue: Q-value estimation for false discovery rate control},
  author = {Storey, John D and Bass, Andrew J and Dabney, Alan and Robinson, David},
  year = {2018},
  note = {R package version 2.14.0},
  url = {http://github.com/jdstorey/qvalue},
}


% science-wide FDR
@ARTICLE{JagerEtAl2013,
  author = {Jager, Leah R and Leek, Jeffrey T},
  title = {Empirical estimates suggest most published medical research is true},
  journal = {Biostatistics},
  year = {2013},
  note={doi: 10.1093/biostatistics/kxt007}
}
@article{BocaEtAl2015,
  title={A regression framework for the proportion of true null hypotheses},
  author={Boca, Simina M and Leek, Jeffrey T},
  journal={bioRxiv},
  pages={035675},
  year={2017},
  publisher={Cold Spring Harbor Labs Journals}
}
@Manual{swfdr2018package,
    title = {swfdr: Science-wise false discovery rate and proportion of true null hypotheses estimation},
    author = {Jeffrey T. Leek and Leah Jager and Simina M. Boca},
    year = {2018},
    note = {R package version 1.3.0}
}
@article{boca2018direct,
  title={A direct approach to estimating false discovery rates conditional on covariates},
  author={Boca, Simina M and Leek, Jeffrey T},
  journal={PeerJ},
  volume={6},
  pages={e6035},
  year={2018},
  publisher={PeerJ Inc.}
}




% Review of methods to control fdr
@article{korthauer2018practical,
  title={A practical guide to methods controlling false discoveries in computational biology},
  author={Korthauer, Keegan and Kimes, Patrick K and Duvallet, Claire and Reyes, Alejandro and Subramanian, Ayshwarya and Teng, Mingxiang and Shukla, Chinmay and Alm, Eric J and Hicks, Stephanie C},
  journal={bioRxiv},
  pages={458786},
  year={2018},
  publisher={Cold Spring Harbor Laboratory}
}


% Datasets
@article{LockeEtAl2015,
  title={Genetic studies of body mass index yield new insights for obesity biology},
  author={Locke, Adam E and Kahali, Bratati and Berndt, Sonja I and Justice, Anne E and Pers, Tune H and Day, Felix R and Powell, Corey and Vedantam, Sailaja and Buchkovich, Martin L and Yang, Jian and others},
  journal={Nature},
  volume={518},
  number={7538},
  pages={197--206},
  year={2015},
  publisher={Nature Publishing Group}
}