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A scalable SCENIC workflow for single-cell gene regulatory network analysis

Bram Van de Sande, Christopher Flerin, Kristofer Davie, Maxime De Waegeneer, Gert Hulselmans, Sara Aibar, Ruth Seurinck, Wouter Saelens, Robrecht Cannoodt, Quentin Rouchon,

Nature Protocols · 2020 · 1.5K citations · 50 references

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50

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

Aravind Subramanian, Pablo Tamayo, Vamsi K. Mootha et al. · Proceedings of the National Academy of Sciences · 2005 · 56.7K citations · Full text

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STAR: ultrafast universal RNA-seq aligner

Alexander Dobin, Carrie Davis, Felix Schlesinger et al. · Bioinformatics · 2012 · 56.2K citations · Full text

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Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

Paul Shannon, Andrew Markiel, Owen Ozier et al. · Genome Research · 2003 · 54.3K citations · Full text

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Visualizing Data using t-SNE

Laurens van der Maaten, Geoffrey E. Hinton · Journal of Machine Learning Research · 2008 · 35.7K citations

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Fast unfolding of communities in large networks

Vincent D. Blondel, Jean‐Loup Guillaume, Renaud Lambiotte et al. · Journal of Statistical Mechanics Theory and Experiment · 2008 · 21.2K citations · Full text

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