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references.bib
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@article{bickel2010,
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}
@article{gtex,
Author={Lonsdale, J. and others},
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Journal="Nature Genetics",
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Month="Jun"
}
@Article{encode,
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Title={{An integrated encyclopedia of DNA elements in the human genome}},
Journal="Nature",
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@article{plotgardener,
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{tidybulk,
author={Mangiola, Stefano
and Molania, Ramyar
and Dong, Ruining
and Doyle, Maria A.
and Papenfuss, Anthony T.},
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}
@article {king_klose,
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citation = {eLife 2017;6:e22631},
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keywords = {pioneer factor, gene regulation, chromatin accessibility, chromatin remodeller, embryonic stem cells, pluripotency},
journal = {eLife},
issn = {2050-084X},
publisher = {eLife Sciences Publications, Ltd},
}
@ARTICLE{Leong2014,
title = "A global non-coding {RNA} system modulates fission yeast protein
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@ARTICLE{Vitting-Seerup2019,
title = "{IsoformSwitchAnalyzeR}: analysis of changes in genome-wide
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}
@ARTICLE{Lee2019,
title = "Plyranges: A grammar of genomic data transformation",
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keywords = "Bioconductor; Data analysis; Genomes; Grammar",
language = "en"
}
@ARTICLE{Lawrence2013,
title = "Software for computing and annotating genomic ranges",
author = "Lawrence, Michael and Huber, Wolfgang and Pag{\`e}s, Herv{\'e}
and Aboyoun, Patrick and Carlson, Marc and Gentleman, Robert and
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}
@ARTICLE{Lee2020,
title = "Fluent genomics with plyranges and tximeta",
author = "Lee, Stuart and Lawrence, Michael and Love, Michael I",
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publisher = "F1000 Research Ltd",
volume = 9,
pages = "109",
month = feb,
year = 2020,
keywords = "Bioconductor; Chromatin Accessibility; Data Integration; Gene
Expression; Workflow; plyranges; tximeta",
language = "en"
}
@article{Mu2023,
author = {Mu, Wancen and Davis, Eric S and Lee, Stuart and Dozmorov, Mikhail G and Phanstiel, Douglas H and Love, Michael I},
title = "{bootRanges: flexible generation of null sets of genomic ranges for hypothesis testing}",
journal = {Bioinformatics},
volume = {39},
number = {5},
year = {2023},
month = {04},
issn = {1367-4811},
doi = {10.1093/bioinformatics/btad190},
url = {https://doi.org/10.1093/bioinformatics/btad190},
note = {btad190}
}
@article{Davis2023,
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}",
journal = {Bioinformatics},
volume = {39},
number = {5},
year = {2023},
month = {04},
issn = {1367-4811},
doi = {10.1093/bioinformatics/btad197},
url = {https://doi.org/10.1093/bioinformatics/btad197},
note = {btad197}
}
@book{Wickham2017,
author = {Wickham, Hadley and Grolemund, Garrett},
day = 05,
edition = 1,
howpublished = {Paperback},
isbn = {1491910399},
month = jan,
publisher = {O'Reilly Media},
title = {R for Data Science: Import, Tidy, Transform, Visualize, and Model Data},
url = {http://r4ds.had.co.nz/},
year = 2017
}
@article{Friedman2010,
title={Regularization Paths for Generalized Linear Models via Coordinate Descent},
volume={33},
url={https://www.jstatsoft.org/index.php/jss/article/view/v033i01},
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journal={Journal of Statistical Software},
author={Friedman, Jerome H. and Hastie, Trevor and Tibshirani, Rob},
year={2010},
pages={1–22}
}
@article{rainer2019,
author = {Rainer, Johannes and Gatto, Laurent and Weichenberger, Christian X},
title = "{ensembldb: an R package to create and use Ensembl-based annotation resources}",
journal = {Bioinformatics},
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number = {17},
pages = {3151-3153},
year = {2019},
month = {01},
issn = {1367-4803},
doi = {10.1093/bioinformatics/btz031},
url = {https://doi.org/10.1093/bioinformatics/btz031},
eprint = {https://academic.oup.com/bioinformatics/article-pdf/35/17/3151/29592004/btz031.pdf},
}
@Article{Alasoo2018,
author={Alasoo, Kaur
and Rodrigues, Julia
and Mukhopadhyay, Subhankar
and Knights, Andrew J.
and Mann, Alice L.
and Kundu, Kousik
and Hale, Christine
and Dougan, Gordon
and Gaffney, Daniel J.
and Consortium, H. I. P. S. C. I.},
title={Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response},
journal={Nature Genetics},
year={2018},
month={Mar},
day={01},
volume={50},
number={3},
pages={424-431},
issn={1546-1718},
doi={10.1038/s41588-018-0046-7},
url={https://doi.org/10.1038/s41588-018-0046-7}
}
@article{Patro2017,
author = {Patro, Rob and Duggal, Geet and Love, Michael I. and Irizarry, Rafael A. and Kingsford, Carl},
journal = {Nature Methods},
title = {Salmon provides fast and bias-aware quantification of transcript expression},
url = {https://doi.org/10.1038/nmeth.4197},
year = 2017
}
@article{Soneson2015,
url = {https://doi.org/10.12688/f1000research.7563.1},
author = {Soneson, Charlotte and Love, Michael I. and Robinson, Mark},
title = {{Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences}},
journal = {F1000Research},
year = 2015,
Volume = 4,
Issue = 1521
}
@article{Love2020,
url = {https://doi.org/10.1371/journal.pcbi.1007664},
author = {Love, Michael I. and Soneson, Charlotte and Hickey, Peter F. and Johnson, Lisa K. and Pierce, N. Tessa and Shepherd, Lori and Morgan, Martin and Patro, Rob},
title = {{Tximeta: Reference sequence checksums for provenance identification in RNA-seq}},
journal = {PLOS Computational Biology},
year = 2020,
volume = 16,
issue = 2,
pages = {e1007664}
}
@article{Segers2023,
author = {Alexandre Segers and Jeroen Gilis and Mattias Van Heetvelde and Elfride De Baere and Lieven Clement},
title = {Juggling offsets unlocks RNA-seq tools for fast scalable differential usage, aberrant splicing and expression analyses},
elocation-id = {2023.06.29.547014},
year = {2023},
doi = {10.1101/2023.06.29.547014},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2023/07/01/2023.06.29.547014},
eprint = {https://www.biorxiv.org/content/early/2023/07/01/2023.06.29.547014.full.pdf},
journal = {bioRxiv}
}