Visualizing and Interpreting Single-Cell Gene Expression Datasets with Similarity Weighted Nonnegative Embedding

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 · 54.5K citations · Full text

Genetics, Genomics, Gene Recognition +23

Visualizing Data using t-SNE

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

Engineering, Data Visualization, Data Exploration +16

Silhouettes: A graphical aid to the interpretation and validation of cluster analysis

Peter J. Rousseeuw · Journal of Computational and Applied Mathematics · 1987 · 19.8K citations

Cluster Computing, Cluster Development, Document Clustering +11

Integrating single-cell transcriptomic data across different conditions, technologies, and species

Andrew Butler, Paul Hoffman, Peter Smibert et al. · Nature Biotechnology · 2018 · 14.1K citations · Full text

Engineering, Genetics, Multiomics +17

Learning the parts of objects by non-negative matrix factorization

Daniel D. Lee, H. Sebastian Seung · Nature · 1999 · 13.8K citations

Non-negative Matrix Factorization, Machine Vision, Image Analysis +11