ctsGE—clustering subgroups of expression data

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Abstract

Summary:

A pre-requisite to clustering noisy data, such as gene-expression data, is the filtering step. As an alternative to this step, the ctsGE R-package applies a sorting step in which all of the data are divided into small groups. The groups are divided according to how the time points are related to the time-series median. Then clustering is performed separately on each group. Thus, the clustering is done in two steps. First, an expression index (i.e. a sequence of 1, −1 and 0) is defined and genes with the same index are grouped together, and then each group of genes is clustered by k-means to create subgroups. The ctsGE package also provides an interactive tool to visualize and explore the gene-expression patterns and their subclusters. ctsGE proposes a way of organizing and exploring expression data without eliminating valuable information.

Availability and Implementation:

Freely available as part of the Bioconductor project at https://bioconductor.org/packages/ctsGE/.

Contact:

ron@agri.gov.il

Supplementary information:

Supplementary data are available at Bioinformatics online.

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