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@article{lee2008novel,
title={Novel low abundance and transient rnas in yeast revealed by tiling microarrays and ultra high--throughput sequencing are not conserved across closely related yeast species},
author={Lee, Albert and Hansen, Kasper Daniel and Bullard, James and Dudoit, Sandrine and Sherlock, Gavin},
journal={PLoS genetics},
volume={4},
number={12},
pages={e1000299},
year={2008},
publisher={Public Library of Science}
}
@article{langmead2009ultrafast,
title={Ultrafast and memory-efficient alignment of short DNA sequences to the human genome},
author={Langmead, Ben and Trapnell, Cole and Pop, Mihai and Salzberg, Steven L},
journal={Genome biology},
volume={10},
number={3},
pages={R25},
year={2009},
publisher={BioMed Central}
}
@misc{sgd,
title = {Saccharomyces Genome Database},
howpublished = {\url{http://www.yeastgenome.org}},
note = {r64}
}
@article{bullard2010evaluation,
title={Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments},
author={Bullard, James H and Purdom, Elizabeth and Hansen, Kasper D and Dudoit, Sandrine},
journal={BMC bioinformatics},
volume={11},
number={1},
pages={94},
year={2010},
publisher={BioMed Central}
}
@article{robinson2010edger,
title={edgeR: a Bioconductor package for differential expression analysis of digital gene expression data},
author={Robinson, Mark D and McCarthy, Davis J and Smyth, Gordon K},
journal={Bioinformatics},
volume={26},
number={1},
pages={139--140},
year={2010},
publisher={Oxford University Press}
}
@article{oshlack2009transcript,
title={Transcript length bias in RNA-seq data confounds systems biology},
author={Oshlack, Alicia and Wakefield, Matthew J},
journal={Biology direct},
volume={4},
number={1},
pages={14},
year={2009},
publisher={BioMed Central}
}
@article{risso2011gc,
title={GC-content normalization for RNA-Seq data},
author={Risso, Davide and Schwartz, Katja and Sherlock, Gavin and Dudoit, Sandrine},
journal={BMC bioinformatics},
volume={12},
number={1},
pages={480},
year={2011},
publisher={BioMed Central}
}
@article{hansen2012removing,
title={Removing technical variability in RNA-seq data using conditional quantile normalization},
author={Hansen, Kasper D and Irizarry, Rafael A and Wu, Zhijin},
journal={Biostatistics},
volume={13},
number={2},
pages={204--216},
year={2012},
publisher={Oxford University Press}
}
@Article{deseq2,
title = {Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
author = {Michael I. Love and Wolfgang Huber and Simon Anders},
year = {2014},
journal = {Genome Biology},
doi = {10.1186/s13059-014-0550-8},
volume = {15},
issue = {12},
pages = {550},
}
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