Guiding biomedical clustering with ClustEval

Nature Protocols
Christian WiwieRichard Röttger

Abstract

Clustering is a popular technique for discovering groups of similar objects in large datasets. It is nowadays applied in all areas of life sciences, from biomedicine to physics. However, designing high-quality cluster analyses is a tedious and complicated task with manifold choices along the way. As a cluster analysis is often the first step of a succeeding downstream analysis, the clustering must be reliable, reproducible, and of the highest quality. To address these challenges, we recently developed ClustEval, an integrated and extensible platform for the automated and standardized design and execution of complex cluster analyses. It allows researchers to design and carry out cluster analyses involving a large number of clustering methods applied to many, large datasets. ClustEval helps to shed light on all major aspects of cluster analysis, from choosing the right similarity function to using validity indices and data preprocessing protocols. Only this high degree of automation allows the researcher to easily run a clustering task with many different tools, parameters, and settings in order to gain the best possible outcome. In this paper, we guide the user step by step through three fundamentally important and widely applic...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jan 15, 2003·BMC Bioinformatics·Gary D Bader, Christopher W V Hogue
Jun 8, 2004·Bioinformatics·A D KingI Jurisica
Jan 16, 2007·Science·Brendan J Frey, Delbert Dueck
Feb 26, 2009·Briefings in Bioinformatics·Bill AndreopoulosMichael Schroeder
May 29, 2010·Nature Methods·Tobias WittkopJan Baumbach
Mar 5, 2011·Nature Protocols·Tobias WittkopJan Baumbach
Mar 20, 2012·Nature Methods·Tamás NepuszAlberto Paccanaro
Jun 28, 2014·Science·Alex Rodriguez, Alessandro Laio
Oct 31, 2014·Scientific Reports·Duong VuVincent Robert
Sep 22, 2015·Nature Methods·Christian WiwieRichard Röttger
Dec 5, 2016·Journal of Molecular Biology·John-Marc ChandoniaSteven E Brenner

❮ Previous
Next ❯

Citations

Jan 5, 2021·Neuroinformatics·Rong Chen
Sep 25, 2021·Scientific Reports·Michael C Thrun

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Pacific Symposium on Biocomputing
Grace T HuangChakra S Chennubhotla
Cold Spring Harbor Protocols
Ram Podicheti, Qunfeng Dong
© 2022 Meta ULC. All rights reserved