17 Bibliography
Aranda, Bruno, Hagen Blankenburg, Samuel Kerrien, Fiona SL Brinkman, Arnaud Ceol, Emilie Chautard, Jose M Dana, et al. 2011. “PSICQUIC and Psiscore: Accessing and Scoring Molecular Interactions.” Nature Methods 8 (7). Nature Publishing Group: 528.
Bray, Nicolas L, Harold Pimentel, Páll Melsted, and Lior Pachter. 2016. “Near-Optimal RNA-Seq Quantification.” Nat. Biotechnol.
Colaprico, A., T. C. Silva, C. Olsen, L. Garofano, C. Cava, D. Garolini, T. S. Sabedot, et al. 2016. “TCGAbiolinks: An R/Bioconductor Package for Integrative Analysis of Tcga Data.” Journal Article. Nucleic Acids Res 44 (8): e71. doi:10.1093/nar/gkv1507.
Collado-Torres, Leonardo, Abhinav Nellore, Kai Kammers, Shannon E Ellis, Margaret A Taub, Kasper D Hansen, Andrew E Jaffe, Ben Langmead, and Jeffrey T Leek. 2017. “Reproducible RNA-seq Analysis Using Recount2.” Nature Biotechnology 35 (4): 319–21. doi:10.1038/nbt.3838.
Davis, Sean R., and Paul S Meltzer. 2007. “GEOquery: A Bridge Between the Gene Expression Omnibus (GEO) and BioConductor.” Bioinformatics 23 (14): 1846–7. doi:10.1093/bioinformatics/btm254.
Demir, Emek, Michael P Cary, Suzanne Paley, Ken Fukuda, Christian Lemer, Imre Vastrik, Guanming Wu, et al. 2010. “The Biopax Community Standard for Pathway Data Sharing.” Nature Biotechnology 28 (9). Nature Publishing Group: 935.
Di Tommaso, Paolo, Maria Chatzou, Evan W Floden, Pablo Prieto Barja, Emilio Palumbo, and Cedric Notredame. 2017. “Nextflow Enables Reproducible Computational Workflows.” Nature Biotechnology 35 (4). Nature Research: 316–19.
Dijk, David van, Juozas Nainys, Roshan Sharma, Pooja Kathail, Ambrose J Carr, Kevin R Moon, Linas Mazutis, Guy Wolf, Smita Krishnaswamy, and Dana Pe’er. 2017. “MAGIC: A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data.” bioRxiv. doi:10.1101/111591.
Fletcher, Russell B, Diya Das, Levi Gadye, Kelly N Street, Ariane Baudhuin, Allon Wagner, Michael B Cole, et al. 2017. “Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution.” Cell Stem Cell 20 (6). Elsevier: 817–830.e8. doi:10.1016/j.stem.2017.04.003.
Ganzfried, Benjamin Frederick, Markus Riester, Benjamin Haibe-Kains, Thomas Risch, Svitlana Tyekucheva, Ina Jazic, Xin Victoria Wang, et al. 2013. “curatedOvarianData: Clinically Annotated Data for the Ovarian Cancer Transcriptome.” Database: The Journal of Biological Databases and Curation 2013 (April): bat013. doi:10.1093/database/bat013.
Green, TRG, and M Petre. 1996. “Usability Analysis of Visual Programming Environments: A ‘Cognitive Dimensions’ Framework.” Journal of Visual Languages & Computing 7 (2): 131–74. doi:10.1006/jvlc.1996.0009.
Grossman, R. L., A. P. Heath, V. Ferretti, H. E. Varmus, D. R. Lowy, W. A. Kibbe, and L. M. Staudt. 2016. “Toward a Shared Vision for Cancer Genomic Data.” Journal Article. N Engl J Med 375 (12): 1109–12. doi:10.1056/NEJMp1607591.
Hardcastle, Thomas, and Krystyna Kelly. 2010. “baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data.” BMC Bioinformatics 11 (1): 422+. doi:10.1186/1471-2105-11-422.
Himes, Blanca E., Xiaofeng Jiang, Peter Wagner, Ruoxi Hu, Qiyu Wang, Barbara Klanderman, Reid M. Whitaker, et al. 2014. “RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.” PloS One 9 (6). doi:10.1371/journal.pone.0099625.
International Cancer Genome, Consortium, T. J. Hudson, W. Anderson, A. Artez, A. D. Barker, C. Bell, R. R. Bernabe, et al. 2010. “International Network of Cancer Genome Projects.” Journal Article. Nature 464 (7291): 993–8. doi:10.1038/nature08987.
Kannan, Lavanya, Marcel Ramos, Angela Re, Nehme El-Hachem, Zhaleh Safikhani, Deena M A Gendoo, Sean Davis, et al. 2016. “Public Data and Open Source Tools for Multi-Assay Genomic Investigation of Disease.” Briefings in Bioinformatics 17 (4): 603–15. doi:10.1093/bib/bbv080.
Köster, Johannes, and Sven Rahmann. 2012. “Snakemake—a Scalable Bioinformatics Workflow Engine.” Bioinformatics 28 (19). Oxford University Press: 2520–2.
Kucera, Mike, Ruth Isserlin, Arkady Arkhangorodsky, and Gary D Bader. 2016. “AutoAnnotate: A Cytoscape App for Summarizing Networks with Semantic Annotations.” F1000Research 5. Faculty of 1000 Ltd.
Langfelder, Peter, and Steve Horvath. 2008. “WGCNA: An R Package for Weighted Correlation Network Analysis.” BMC Bioinformatics 9 (1). BioMed Central: 559.
Lappalainen, Tuuli, Michael Sammeth, Marc R. Friedländer, Peter A. C. ’t Hoen, Jean Monlong, Manuel A. Rivas, Mar Gonzàlez-Porta, et al. 2013. “Transcriptome and Genome Sequencing Uncovers Functional Variation in Humans.” Nature, no. 501: 506–11.
Law, Charity W., Yunshun Chen, Wei Shi, and Gordon K. Smyth. 2014. “Voom: precision weights unlock linear model analysis tools for RNA-seq read counts.” Genome Biology 15 (2). BioMed Central Ltd: R29+. doi:10.1186/gb-2014-15-2-r29.
Lawrence, Michael, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin Morgan, and Vincent Carey. 2013. “Software for Computing and Annotating Genomic Ranges.” PLoS Comput. Biol. 9. doi:10.1371/journal.pcbi.1003118.
Lee, Stuart, Dianne Cook, and Michael Lawrence. 2018. “Plyranges: A Grammar of Genomic Data Transformation.” bioRxiv. Cold Spring Harbor Laboratory. doi:10.1101/327841.
Leng, N., J. A. Dawson, J. A. Thomson, V. Ruotti, A. I. Rissman, B. M. G. Smits, J. D. Haag, M. N. Gould, R. M. Stewart, and C. Kendziorski. 2013. “EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.” Bioinformatics 29 (8). Oxford University Press: 1035–43. doi:10.1093/bioinformatics/btt087.
Li, B., and C. N. Dewey. 2011. “RSEM: Accurate Transcript Quantification from Rna-Seq Data with or Without a Reference Genome.” Journal Article. BMC Bioinformatics 12: 323. doi:10.1186/1471-2105-12-323.
Li, Bo, and Colin N. Dewey. 2011. “RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.” BMC Bioinformatics 12: 323+. doi:10.1186/1471-2105-12-3231.
Love, Michael. 2018. Airway: RangedSummarizedExperiment for Rna-Seq in Airway Smooth Muscle Cells, by Himes et Al Plos One 2014.
Love, Michael I., Wolfgang Huber, and Simon Anders. 2014. “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology 15 (12). BioMed Central Ltd: 550+. doi:10.1186/s13059-014-0550-8.
Luna, Augustin, Özgün Babur, Bülent Arman Aksoy, Emek Demir, and Chris Sander. 2015. “PaxtoolsR: Pathway Analysis in R Using Pathway Commons.” Bioinformatics 32 (8). Oxford University Press: 1262–4.
Merico, Daniele, Ruth Isserlin, Oliver Stueker, Andrew Emili, and Gary D Bader. 2010. “Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation.” PloS One 5 (11). Public Library of Science: e13984.
Morgan, Martin. 2018. AnnotationHub: Client to Access Annotationhub Resources.
Morgan, Xochitl C, and Curtis Huttenhower. 2012. “Chapter 12: Human Microbiome Analysis.” PLoS Computational Biology 8 (12): e1002808. doi:10.1371/journal.pcbi.1002808.
Morris, John H, Leonard Apeltsin, Aaron M Newman, Jan Baumbach, Tobias Wittkop, Gang Su, Gary D Bader, and Thomas E Ferrin. 2011. “ClusterMaker: A Multi-Algorithm Clustering Plugin for Cytoscape.” BMC Bioinformatics 12 (1). BioMed Central: 436.
Mostafavi, Sara, Debajyoti Ray, David Warde-Farley, Chris Grouios, and Quaid Morris. 2008. “GeneMANIA: A Real-Time Multiple Association Network Integration Algorithm for Predicting Gene Function.” Genome Biology 9 (1). BioMed Central: S4.
Oesper, Layla, Daniele Merico, Ruth Isserlin, and Gary D Bader. 2011. “WordCloud: A Cytoscape Plugin to Create a Visual Semantic Summary of Networks.” Source Code for Biology and Medicine 6 (1). BioMed Central: 7.
Ono, Keiichiro, Tanja Muetze, Georgi Kolishovski, Paul Shannon, and Barry Demchak. 2015. “CyREST: Turbocharging Cytoscape Access for External Tools via a Restful Api.” F1000Research 4. Faculty of 1000 Ltd.
Pasolli, Edoardo, Lucas Schiffer, Paolo Manghi, Audrey Renson, Valerie Obenchain, Duy Tin Truong, Francesco Beghini, et al. 2017. “Accessible, Curated Metagenomic Data Through ExperimentHub.” Nature Methods 14 (11). Nature Research: 1023–4. doi:10.1038/nmeth.4468.
Patro, Rob, Geet Duggal, Michael I Love, Rafael A Irizarry, and Carl Kingsford. 2017. “Salmon Provides Fast and Bias-Aware Quantification of Transcript Expression.” Nat. Methods 14 (6~mar): 417–19.
Patro, Rob, Stephen M. Mount, and Carl Kingsford. 2014. “Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.” Nature Biotechnology 32: 462–64. doi:10.1038/nbt.2862.
Pierson, Emma, and Christopher Yau. 2015. “ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis.” Genome Biology 16 (1): 241. doi:10.1186/s13059-015-0805-z.
Pratt, Dexter, Jing Chen, Rudolf Pillich, Vladimir Rynkov, Aaron Gary, Barry Demchak, and Trey Ideker. 2017. “NDEx 2.0: A Clearinghouse for Research on Cancer Pathways.” Cancer Research 77 (21). AACR: e58–e61.
Quinlan, Aaron R, and Ira M Hall. 2010. “BEDTools: A Flexible Suite of Utilities for Comparing Genomic Features.” Bioinformatics 26 (6): 841–42. doi:10.1093/bioinformatics/btq033.
Ramos, Marcel, Lucas Schiffer, Angela Re, Rimsha Azhar, Azfar Basunia, Carmen Rodriguez, Tiffany Chan, et al. 2017. “Software for the Integration of Multiomics Experiments in Bioconductor.” Cancer Research 77 (21). American Association for Cancer Research: e39–e42. doi:10.1158/0008-5472.CAN-17-0344.
Reimand, Jüri, Tambet Arak, Priit Adler, Liis Kolberg, Sulev Reisberg, Hedi Peterson, and Jaak Vilo. 2016. “G: Profiler—a Web Server for Functional Interpretation of Gene Lists (2016 Update).” Nucleic Acids Research 44 (W1). Oxford University Press: W83–W89.
Risso, Davide, Fanny Perraudeau, Svetlana Gribkova, Sandrine Dudoit, and Jean-Philippe Vert. 2018a. “A General and Flexible Method for Signal Extraction from Single-Cell Rna-Seq Data.” Nature Communications 9 (1): 284. https://doi.org/10.1038/s41467-017-02554-5.
———. 2018b. “A General and Flexible Method for Signal Extraction from Single-Cell Rna-Seq Data.” Nature Communications 9 (1): 284.
Roadmap Epigenomics Consortium, Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, et al. 2015. “Integrative Analysis of 111 Reference Human Epigenomes.” Nature 518 (7539): 317–30. doi:10.1038/nature14248.
Robert, Christelle, and Mick Watson. 2015. “Errors in RNA-Seq quantification affect genes of relevance to human disease.” Genome Biology. doi:10.1186/s13059-015-0734-x.
Robinson, M. D., D. J. McCarthy, and G. K. Smyth. 2009. “edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.” Bioinformatics 26 (1). Oxford University Press: 139–40. doi:10.1093/bioinformatics/btp616.
Schiffer, Lucas, Rimsha Azhar, Lori Shepherd, Marcel Ramos, Ludwig Geistlinger, Curtis Huttenhower, Jennifer B Dowd, Nicola Segata, and Levi Waldron. 2018. “HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor.” bioRxiv. doi:10.1101/299115.
Settle, Brett, David Otasek, John H Morris, and Barry Demchak. 2018. “AMatReader: Importing Adjacency Matrices via Cytoscape Automation.” F1000Research 7.
Shannon, Paul, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, and Trey Ideker. 2003. “Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks.” Genome Research 13 (11). Cold Spring Harbor Lab: 2498–2504.
Soneson, Charlotte, Michael I. Love, and Mark Robinson. 2015. “Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences.” F1000Research 4 (1521). doi:10.12688/f1000research.7563.1.
Stephens, Matthew. 2016. “False Discovery Rates: A New Deal.” Biostatistics 18 (2). https://doi.org/10.1093/biostatistics/kxw041.
Street, Kelly, Davide Risso, Russell B Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, and Sandrine Dudoit. 2018. “Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics.” BMC Genomics 19 (1): 477.
Szklarczyk, Damian, John H Morris, Helen Cook, Michael Kuhn, Stefan Wyder, Milan Simonovic, Alberto Santos, et al. 2016. “The String Database in 2017: Quality-Controlled Protein–protein Association Networks, Made Broadly Accessible.” Nucleic Acids Research. Oxford University Press, gkw937.
Trapnell, Cole, David G Hendrickson, Martin Sauvageau, Loyal Goff, John L Rinn, and Lior Pachter. 2013. “Differential analysis of gene regulation at transcript resolution with RNA-seq.” Nature Biotechnology. doi:10.1038/nbt.2450.
Tseng, George C., and Wing H. Wong. 2005. “Tight Clustering: A Resampling-Based Approach for Identifying Stable and Tight Patterns in Data.” Biometrics 61 (1): 10–16. doi:10.1111/j.0006-341X.2005.031032.x.
Van den Berge, Koen, Fanny Perraudeau, Charlotte Soneson, Michael I. Love, Davide Risso, Jean-Philippe Vert, Mark D. Robinson, Sandrine Dudoit, and Lieven Clement. 2018. “Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications.” Genome Biology 19 (1). https://doi.org/10.1186/s13059-018-1406-4.
Verhaak, R. G., P. Tamayo, J. Y. Yang, D. Hubbard, H. Zhang, C. J. Creighton, S. Fereday, et al. 2013. “Prognostically Relevant Gene Signatures of High-Grade Serous Ovarian Carcinoma.” Journal Article. J Clin Invest 123 (1): 517–25. doi:10.1172/JCI65833.
Wang, K., D. Singh, Z. Zeng, S. J. Coleman, Y. Huang, G. L. Savich, X. He, et al. 2010. “MapSplice: Accurate Mapping of Rna-Seq Reads for Splice Junction Discovery.” Journal Article. Nucleic Acids Res 38 (18): e178. doi:10.1093/nar/gkq622.
Wickham, Hadley. 2014. “Tidy Data.” Journal of Statistical Software, Articles 59 (10): 1–23. doi:10.18637/jss.v059.i10.
Wu, Hao, Chi Wang, and Zhijin Wu. 2013. “A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data.” Biostatistics 14 (2). Oxford University Press: 232–43. doi:10.1093/biostatistics/kxs033.
Zappia, Luke, Belinda Phipson, and Alicia Oshlack. 2017. “Splatter: simulation of single-cell RNA sequencing data.” Genome Biology 18 (174). https://doi.org/10.1186/s13059-017-1305-0.
Zhu, Anqi, Joseph G. Ibrahim, and Michael I. Love. 2018. “Heavy-Tailed Prior Distributions for Sequence Count Data: Removing the Noise and Preserving Large Differences.” bioRxiv. https://doi.org/10.1101/303255.