bcbio_rnaseq.bib

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title = {{Kraken: ultrafast metagenomic sequence classification using exact alignments.}},
journal = {Genome biology},
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@article{Yang:2002ty,
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@article{Love:2015kw,
author = {Love, Michael I and Anders, Simon and Kim, Vladislav and Huber, Wolfgang},
title = {{RNA-Seq workflow: gene-level exploratory analysis and differential expression.}},
journal = {F1000Research},
year = {2015},
volume = {4},
pages = {1070}
}

@article{Dobin:2016kq,
author = {Dobin, Alexander and Gingeras, Thomas R},
title = {{Optimizing RNA-Seq Mapping with STAR.}},
journal = {Methods in molecular biology (Clifton, N.J.)},
year = {2016},
volume = {1415},
number = {Chapter 13},
pages = {245--262}
}

@manual{pheatmap,
title = {{pheatmap: Pretty Heatmaps}},
author = {Kolde, Raivo},
year = {2015},
annote = {R package version 1.0.8}
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@article{Conesa:2016du,
author = {Conesa, Ana and Madrigal, Pedro and Tarazona, Sonia and Gomez-Cabrero, David and Cervera, Alejandra and McPherson, Andrew and Szcze{\'{s}}niak, Micha{\l} Wojciech and Gaffney, Daniel J and Elo, Laura L and Zhang, Xuegong and Mortazavi, Ali},
title = {{A survey of best practices for RNA-seq data analysis.}},
journal = {Genome biology},
year = {2016},
volume = {17},
number = {1},
pages = {13},
month = jan
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@article{Li:2012cx,
author = {Li, Wentian},
title = {{Volcano plots in analyzing differential expressions with mRNA microarrays.}},
journal = {Journal of bioinformatics and computational biology},
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@manual{RStudio,
title = {{RStudio: Integrated Development Environment for R}},
author = {{RStudio Team}},
organization = {RStudio, Inc.},
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@article{PEAR,
author = {Zhang, Jiajie and Kobert, Kassian and Flouri, Tom{\'a}{\v s} and Stamatakis, Alexandros},
title = {{PEAR: a fast and accurate Illumina Paired-End reAd mergeR.}},
journal = {Bioinformatics},
year = {2014},
volume = {30},
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month = mar
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@article{sleuth,
author = {Pimentel, Harold J and Bray, Nicolas and Puente, Suzette and Melsted, P{\'a}ll and Pachter, Lior},
title = {{Differential analysis of RNA-Seq incorporating quantification uncertainty}},
journal = {bioRxiv},
year = {2016}
}

@article{tximport,
author = {Soneson, Charlotte and Love, Michael I and Robinson, Mark D},
title = {{Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences}},
journal = {F1000Research},
year = {2016},
volume = {4},
pages = {1521},
month = feb
}

@article{Staedtler:2013eg,
author = {Staedtler, Frank and Hartmann, Nicole and Letzkus, Martin and Bongiovanni, Sandrine and Scherer, Andreas and Marc, Philippe and Johnson, Keith J and Schumacher, Martin M},
title = {{Robust and tissue-independent gender-specific transcript biomarkers.}},
journal = {Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals},
year = {2013},
volume = {18},
number = {5},
pages = {436--445},
month = aug
}

@article{sailfish,
author = {Patro, Rob and Mount, Stephen M and Kingsford, Carl},
title = {{Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.}},
journal = {Nature biotechnology},
year = {2014},
volume = {32},
number = {5},
pages = {462--464},
month = may
}

@article{salmon,
author = {Patro, Rob and Duggal, Geet and Love, Michael I and Irizarry, Rafael A and Kingsford, Carl},
title = {{Salmon provides fast and bias-aware quantification of transcript expression.}},
journal = {Nature methods},
year = {2017},
volume = {31},
number = {4},
pages = {3881--419},
month = mar
}

@article{VandenBerge:2017fe,
author = {Van den Berge, Koen and Soneson, Charlotte and Robinson, Mark D and Clement, Lieven},
title = {{A general and powerful stage-wise testing procedure for differential expression and differential transcript usage}},
journal = {bioRxiv},
year = {2017},
pages = {109082},
month = feb
}

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title = {{Statistical tests for differential expression in cDNA microarray experiments.}},
journal = {Genome biology},
year = {2003},
volume = {4},
number = {4},
pages = {210}
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@article{Langaas:2005vn,
author = {Langaas, Mette and Lindqvist, Bo Henry and Ferkingstad, Egil},
title = {{Estimating the Proportion of True Null Hypotheses, with Application to DNA Microarray Data}},
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@article{DESeq2,
author = {Love, Michael I and Huber, Wolfgang and Anders, Simon},
title = {{Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.}},
journal = {Genome biology},
year = {2014},
volume = {15},
number = {12},
pages = {550}
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@article{STAR,
author = {Dobin, Alexander and Davis, Carrie A and Schlesinger, Felix and Drenkow, Jorg and Zaleski, Chris and Jha, Sonali and Batut, Philippe and Chaisson, Mark and Gingeras, Thomas R},
title = {{STAR: ultrafast universal RNA-seq aligner.}},
journal = {Bioinformatics},
year = {2013},
volume = {29},
number = {1},
pages = {15--21},
month = jan
}

@book{Hilbe:2011ua,
author = {Hilbe, Joseph M},
title = {{Negative Binomial Regression}},
publisher = {Cambridge University Press},
year = {2011},
address = {Cambridge}
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@article{Karyagyna:2010th,
author = {Karyagyna, Anna S and Vassiliev, Michail O and Ershova, Anna S and Nurtdinov, Ramil N and Lossev, Ilya S},
title = {{Probe-Level Universal Search (PLUS) algorithm for gender differentiation in affymetrix datasets.}},
journal = {Journal of bioinformatics and computational biology},
year = {2010},
volume = {8},
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month = jun
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@book{ggplot2,
author = {Wickham, Hadley},
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publisher = {Springer New York},
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@article{Robinson:2010dd,
author = {Robinson, Mark D and Oshlack, Alicia},
title = {{A scaling normalization method for differential expression analysis of RNA-seq data.}},
journal = {Genome biology},
year = {2010},
volume = {11},
number = {3},
pages = {R25}
}

@book{Jolliffe:2002aa,
author = {Jolliffe, Ian},
title = {{Principal component analysis}},
publisher = {Wiley Online Library},
year = {2002}
}

@article{reshape2,
author = {Wickham, Hadley},
title = {{Reshaping Data with the reshape Package}},
journal = {Journal of Statistical Software},
year = {2007},
volume = {21},
number = {12},
pages = {1--20}
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@article{Cox:1987fu,
author = {Cox, D R and Reid, N},
title = {{Parameter Orthogonality and Approximate Conditional Inference}},
journal = {Journal of the Royal Statistical Society. Series B (Methodological)},
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@article{Li:2014fv,
author = {Li, Wentian and Freudenberg, Jan and Suh, Young Ju and Yang, Yaning},
title = {{Using volcano plots and regularized-chi statistics in genetic association studies.}},
journal = {Computational biology and chemistry},
year = {2014},
volume = {48},
pages = {77--83},
month = feb
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@article{Wang:2009di,
author = {Wang, Zhong and Gerstein, Mark and Snyder, Michael},
title = {{RNA-Seq: a revolutionary tool for transcriptomics.}},
journal = {Nature reviews. Genetics},
year = {2009},
volume = {10},
number = {1},
pages = {57--63},
month = jan
}