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	title = {bootRanges: Flexible generation of null sets of genomic ranges for hypothesis testing},
	year = {2023},
	doi = {10.1093/bioinformatics/btad190},
	journal = {Bioinformatics}
}

@article{matchRanges,
	author = {Davis, Eric S. and Mu, Wancen and Lee, Stuart and Dozmorov, Mikhail G. and Love, Michael I. and Phanstiel, Douglas H.},
	title = {matchRanges: Generating null hypothesis genomic ranges via covariate-matched sampling},
	year = {2023},
	doi = {10.1093/bioinformatics/btad197},
	journal = {Bioinformatics}
}

@article{excluderanges,
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	title = {excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies},
	year = {2023},
	doi = {10.1093/bioinformatics/btad198},
	journal = {Bioinformatics}
}

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pmcid = {PMC4271068}
}

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}

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urldate = {2017-11-01},
journal = {The annals of applied statistics},
volume = {4},
number = {4},
issn = {1932-6157},
doi = {10.1214/10-{AOAS363}}
}

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author={McLean, Cory Y.
and Bristor, Dave
and Hiller, Michael
and Clarke, Shoa L.
and Schaar, Bruce T.
and Lowe, Craig B.
and Wenger, Aaron M.
and Bejerano, Gill},
title={GREAT improves functional interpretation of cis-regulatory regions},
journal={Nature Biotechnology},
year={2010},
month={May},
day={01},
volume={28},
number={5},
pages={495-501},
issn={1546-1696},
doi={10.1038/nbt.1630},
url={https://doi.org/10.1038/nbt.1630}
}

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journal = {{PLoS} Computational Biology},
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number = {5},
doi = {10.1371/journal.pcbi.1002529},
pmid = {22693437},
pmcid = {PMC3364938}
}

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    title = "{ChIP-Enrich: gene set enrichment testing for ChIP-seq data}",
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    eprint = {https://academic.oup.com/nar/article-pdf/42/13/e105/25361469/gku463.pdf},
}

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    volume = {9},
    url = {https://doi.org/10.1371/journal.pcbi.1003118},
    pages = {1-10},
    number = {8}
}

@article{dnacopy,
   Author="Olshen, A. B.  and Venkatraman, E. S.  and Lucito, R.  and Wigler, M. ",
   Title="{{C}ircular binary segmentation for the analysis of array-based {D}{N}{A} copy number data}",
   Journal="Biostatistics",
   Year="2004",
   Volume="5",
   Number="4",
   Pages="557--572",
   Month="Oct"
}

@article{ensembl2021,
    author = {Howe, Kevin L and Achuthan, Premanand and Allen, James and Allen, Jamie and Alvarez-Jarreta, Jorge and Amode, M Ridwan and Armean, Irina M and Azov, Andrey G and Bennett, Ruth and Bhai, Jyothish and Billis, Konstantinos and Boddu, Sanjay and Charkhchi, Mehrnaz and Cummins, Carla and Da Rin Fioretto, Luca and Davidson, Claire and Dodiya, Kamalkumar and El Houdaigui, Bilal and Fatima, Reham and Gall, Astrid and Garcia Giron, Carlos and Grego, Tiago and Guijarro-Clarke, Cristina and Haggerty, Leanne and Hemrom, Anmol and Hourlier, Thibaut and Izuogu, Osagie G and Juettemann, Thomas and Kaikala, Vinay and Kay, Mike and Lavidas, Ilias and Le, Tuan and Lemos, Diana and Gonzalez Martinez, Jose and Marugán, José Carlos and Maurel, Thomas and McMahon, Aoife C and Mohanan, Shamika and Moore, Benjamin and Muffato, Matthieu and Oheh, Denye N and Paraschas, Dimitrios and Parker, Anne and Parton, Andrew and Prosovetskaia, Irina and Sakthivel, Manoj P and Salam, Ahamed I Abdul and Schmitt, Bianca M and Schuilenburg, Helen and Sheppard, Dan and Steed, Emily and Szpak, Michal and Szuba, Marek and Taylor, Kieron and Thormann, Anja and Threadgold, Glen and Walts, Brandon and Winterbottom, Andrea and Chakiachvili, Marc and Chaubal, Ameya and De Silva, Nishadi and Flint, Bethany and Frankish, Adam and Hunt, Sarah E and IIsley, Garth R and Langridge, Nick and Loveland, Jane E and Martin, Fergal J and Mudge, Jonathan M and Morales, Joanella and Perry, Emily and Ruffier, Magali and Tate, John and Thybert, David and Trevanion, Stephen J and Cunningham, Fiona and Yates, Andrew D and Zerbino, Daniel R and Flicek, Paul},
    title = "{Ensembl 2021}",
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    number = {D1},
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    year = {2020},
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    issn = {0305-1048},
    doi = {10.1093/nar/gkaa942},
    url = {https://doi.org/10.1093/nar/gkaa942}
}

@article{ensembldb,
    author = {Rainer, Johannes and Gatto, Laurent and Weichenberger, Christian X},
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    journal = {Bioinformatics},
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    number = {17},
    pages = {3151-3153},
    year = {2019},
    month = {01},
    abstract = "{Bioinformatics research frequently involves handling gene-centric data such as exons, transcripts, proteins and their positions relative to a reference coordinate system. The ensembldb Bioconductor package retrieves and stores Ensembl-based genetic annotations and positional information, and furthermore offers identifier conversion and coordinates mappings for gene-associated data. In support of reproducible research, data are tied to Ensembl releases and are kept separately from the software. Premade data packages are available for a variety of genomes and Ensembl releases. Three examples demonstrate typical use cases of this software.ensembldb is part of Bioconductor (https://bioconductor.org/packages/ensembldb).Supplementary data are available at Bioinformatics online.}",
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btz031},
    url = {https://doi.org/10.1093/bioinformatics/btz031}
}

@Article{encode,
author={ENCODE},
title={{An integrated encyclopedia of DNA elements in the human genome}},
journal={Nature},
year={2012},
month={Sep},
day={01},
volume={489},
number={7414},
pages={57-74},
issn={1476-4687},
doi={10.1038/nature11247},
url={https://doi.org/10.1038/nature11247}
}

@Article{Lee2019,
author={Lee, Stuart
and Cook, Dianne
and Lawrence, Michael},
title={plyranges: a grammar of genomic data transformation},
journal={Genome Biology},
year={2019},
month={Jan},
day={04},
volume={20},
number={1},
pages={4},
issn={1474-760X},
doi={10.1186/s13059-018-1597-8},
url={https://doi.org/10.1186/s13059-018-1597-8}
}

@article {Kramer2022,
    author = {Kramer, Nicole E and Davis, Eric S and Wenger, Craig D and Deoudes, Erika M and Parker, Sarah M and Love, Michael I and Phanstiel, Douglas H},
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}

@article{dozmorov2017,
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    title = "{Epigenomic annotation-based interpretation of genomic data: from enrichment analysis to machine learning}",
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}

@article{ferkingstad2015,
author = {Egil Ferkingstad and Lars Holden and Geir Kjetil Sandve},
title = {{Monte Carlo Null Models for Genomic Data}},
volume = {30},
journal = {Statistical Science},
number = {1},
publisher = {Institute of Mathematical Statistics},
pages = {59 -- 71},
keywords = {genomics, Hypothesis testing, Monte Carlo methods},
year = {2015},
doi = {10.1214/14-STS484},
URL = {https://doi.org/10.1214/14-STS484}
}


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    title = "{OLOGRAM: determining significance of total overlap length between genomic regions sets}",
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    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btz810},
    url = {https://doi.org/10.1093/bioinformatics/btz810},
    eprint = {https://academic.oup.com/bioinformatics/article-pdf/36/6/1920/32915137/btz810.pdf},
}

@Article{fluent,
AUTHOR = { Lee, S and Lawrence, M and Love, MI},
TITLE = {Fluent genomics with plyranges and tximeta [version 1; peer review: 1 approved, 2 approved with reservations]
},
JOURNAL = {F1000Research},
VOLUME = {9},
YEAR = {2020},
NUMBER = {109},
DOI = {10.12688/f1000research.22259.1}
}
