R/bibliography.R

In tidybulk: Brings transcriptomics to the tidyverse

my_bibliography = function() {
	list(
	tidyverse = "@article{wickham2019welcome,
  title={Welcome to the Tidyverse},
  author={Wickham, Hadley and Averick, Mara and Bryan, Jennifer and Chang, Winston and McGowan, Lucy D'Agostino and Francois, Romain and Grolemund, Garrett and Hayes, Alex and Henry, Lionel and Hester, Jim and others},
  journal={Journal of Open Source Software},
  volume={4},
  number={43},
  pages={1686},
  year={2019}
	}",
	featurecounts = "@article{liao2014featurecounts,
  title={featureCounts: an efficient general purpose program for assigning sequence reads to genomic features},
  author={Liao, Yang and Smyth, Gordon K and Shi, Wei},
  journal={Bioinformatics},
  volume={30},
  number={7},
  pages={923--930},
  year={2014},
  publisher={Oxford University Press}
	}" ,
	edger = "@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}
	}",
	tmm = "@article{robinson2010scaling,
  title={A scaling normalization method for differential expression analysis of RNA-seq data},
  author={Robinson, Mark D and Oshlack, Alicia},
  journal={Genome biology},
  volume={11},
  number={3},
  pages={1--9},
  year={2010},
  publisher={BioMed Central}
	}",
	limma = "@incollection{smyth2005limma,
  title={Limma: linear models for microarray data},
  author={Smyth, Gordon K},
  booktitle={Bioinformatics and computational biology solutions using R and Bioconductor},
  pages={397--420},
  year={2005},
  publisher={Springer}
	}",
	deseq2 = "@article{love2014moderated,
  title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
  author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
  journal={Genome biology},
  volume={15},
  number={12},
  pages={550},
  year={2014},
  publisher={Springer}
	}",
	survival = "@book{Grambsch2000-oo,
	  title   = {Modeling survival data: extending the Cox model},
	  author  = {Grambsch, Patricia M and Therneau, Terry M},
	  journal = {Stat. Biol. Health},
	  year    =  2000
	}",
	boot = "@book{davison1997bootstrap,
  title={Bootstrap methods and their application},
  author={Davison, Anthony Christopher and Hinkley, David Victor},
  number={1},
  year={1997},
  publisher={Cambridge university press}
	}",
	betareg = "@article{cribari2009beta,
  title={Beta regression in R},
  author={Cribari-Neto, Francisco and Zeileis, Achim},
  year={2009},
  publisher={Department of Statistics and Mathematics x, WU Vienna University}
	}",
	stats = "  @Manual{,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2020},
    url = {https://www.R-project.org/},
  }",
	seurat = "@article{Butler2018-ae,
  title    = {Integrating single-cell transcriptomic data across different
	conditions, technologies, and species},
  author   = {Butler, Andrew and Hoffman, Paul and Smibert, Peter and Papalexi,
	Efthymia and Satija, Rahul},
  journal  = {Nat. Biotechnol.},
  volume   =  36,
  number   =  5,
  pages    = {411--420},
  month    =  jun,
  year     =  2018,
  language = {en}
	}",
	rtsne = "  @Article{,
    title = {Visualizing High-Dimensional Data Using t-SNE},
    volume = {9},
    pages = {2579-2605},
    year = {2008},
    author = {L.J.P. {van der Maaten} and G.E. Hinton},
    journal = {Journal of Machine Learning Research},
  }",
	widyr ="@Manual{,
    title = {widyr: Widen, Process, then Re-Tidy Data},
    author = {David Robinson},
    year = {2020},
    note = {R package version 0.1.3},
    url = {https://CRAN.R-project.org/package=widyr},
  }",
	cibersort = "@article{newman2015robust,
  title={Robust enumeration of cell subsets from tissue expression profiles},
  author={Newman, Aaron M and Liu, Chih Long and Green, Michael R and Gentles, Andrew J and Feng, Weiguo and Xu, Yue and Hoang, Chuong D and Diehn, Maximilian and Alizadeh, Ash A},
  journal={Nature methods},
  volume={12},
  number={5},
  pages={453--457},
  year={2015},
  publisher={Nature Publishing Group}
	}",
	sva = "@article{leek2012sva,
  title={The sva package for removing batch effects and other unwanted variation in high-throughput experiments},
  author={Leek, Jeffrey T and Johnson, W Evan and Parker, Hilary S and Jaffe, Andrew E and Storey, John D},
  journal={Bioinformatics},
  volume={28},
  number={6},
  pages={882--883},
  year={2012},
  publisher={Oxford University Press}
	}",
	clusterProfiler = "@Article{,
    title = {clusterProfiler: an R package for comparing biological themes among gene clusters},
    author = {Guangchuang Yu and Li-Gen Wang and Yanyan Han and Qing-Yu He},
    journal = {OMICS: A Journal of Integrative Biology},
    year = {2012},
    volume = {16},
    number = {5},
    pages = {284-287},
    pmid = {22455463},
    doi = {10.1089/omi.2011.0118},
  }",
	msigdbr = c( "@Manual{,
    title = {msigdbr: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format},
    author = {Igor Dolgalev},
    year = {2020},
    note = {R package version 7.1.1},
    url = {https://CRAN.R-project.org/package=msigdbr},
  }",
	"@article{liberzon2011molecular,
  title={Molecular signatures database (MSigDB) 3.0},
  author={Liberzon, Arthur and Subramanian, Aravind and Pinchback, Reid and Thorvaldsdottir, Helga and Tamayo, Pablo and Mesirov, Jill P},
  journal={Bioinformatics},
  volume={27},
  number={12},
  pages={1739--1740},
  year={2011},
  publisher={Oxford University Press}
	}")
)
}