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@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{Srivastava2019,
title={{Alevin efficiently estimates accurate gene abundances from dscRNA-seq data}},
author={Srivastava, Avi and Malik, Laraib and Smith, Tom Sean and Sudbery, Ian and Patro, Rob},
journal={Genome Biology},
year={2019},
volume={20},
number={65},
url={https://doi.org/10.1186/s13059-019-1670-y}
}
@article{ensembldb,
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},
year = {2019},
month = {01}
}
@article{granges,
author = {Lawrence, Michael AND Huber, Wolfgang AND Pagès, Hervé AND Aboyoun, Patrick AND Carlson, Marc AND Gentleman, Robert AND Morgan, Martin T. AND Carey, Vincent J.},
journal = {PLOS Computational Biology},
publisher = {Public Library of Science},
title = {{Software for Computing and Annotating Genomic Ranges}},
year = {2013},
month = {08},
volume = {9},
pages = {1-10},
number = {8}
}
@article {Orjuelag2019,
author = {Orjuela, Stephany and Huang, Ruizhu and Hembach, Katharina M. and Robinson, Mark D. and Soneson, Charlotte},
title = {{ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data}},
year = {2019},
publisher = {G3: Genes, Genomes, Genetics},
journal = {G3: Genes, Genomes, Genetics}
}
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