Application of HDBSСAN Method for Clustering scRNA-seq Data
Maria Andreevna AKIMENKOVA,
Anna Anatolyevna MAZNINA,
Anton Yurievich NAUMOV,
Evgeny Andreevich KARPULEVICH https://doi.org/10.15514/ISPRAS-2020-32(5)-8
Abstract
One of the main tasks in the analysis of single cell RNA sequencing (scRNA-seq) data is the identification of cell types and subtypes, which is usually based on some method of clustering. There is a number of generally accepted approaches to solving the clustering problem, one of which is implemented in the Seurat package. In addition, the quality of clustering is influenced by the use of preprocessing algorithms, such as imputation, dimensionality reduction, feature selection, etc. In the article, the HDBSCAN hierarchical clustering method is used to cluster scRNA-seq data. For a more complete comparison Experiments and comparisons were made on two labeled datasets: Zeisel (3005 cells) and Romanov (2881 cells). To compare the quality of clustering, two external metrics were used: Adjusted Rand index and V-measure. The experiments demonstrated a higher quality of clustering by the HDBSCAN method on the Zeisel dataset and a poorer quality on the Romanov dataset.
About the Authors
Maria Andreevna AKIMENKOVA
Ivannikov Institute for System Programming of the Russian Academy of Sciences,
Moscow Institute of Physics and Technology
Russian Federation
Laboratory assistant, Information Systems Department
Russian Federation
Laboratory assistant, Information Systems Department
Anna Anatolyevna MAZNINA
Moscow Institute of Physics and Technology
Russian Federation
Laboratory assistant at the Genomic Engineering Laboratory
Russian Federation
Laboratory assistant at the Genomic Engineering Laboratory
Anton Yurievich NAUMOV
Ivannikov Institute for System Programming of the Russian Academy of Sciences
Russian Federation
Research assistant, Information Systems Department
Russian Federation
Research assistant, Information Systems Department
Evgeny Andreevich KARPULEVICH
Ivannikov Institute for System Programming of the Russian Academy of Sciences,
Moscow Institute of Physics and Technology
Russian Federation
Researcher, Information Systems Department
Russian Federation
Researcher, Information Systems Department
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Review
For citations:
AKIMENKOVA M.A., MAZNINA A.A., NAUMOV A.Yu., KARPULEVICH E.A. Application of HDBSСAN Method for Clustering scRNA-seq Data. Proceedings of the Institute for System Programming of the RAS (Proceedings of ISP RAS). 2020;32(5):111-120. https://doi.org/10.15514/ISPRAS-2020-32(5)-8
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