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HTSCluster paper published in Bioinformatics

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Our work describing a method for co-expression analyses of RNA-seq data using our R package HTSCluster was recently published in Bioinformatics (doi: 10.1093/bioinformatics/btu845). Abstract below…

Motivation: In recent years gene expression studies have increasingly made use of high-throughput sequencing technology. In turn, research concerning the appropriate statistical methods for the analysis of digital gene expression has flourished, primarily in the context of normalization and differential analysis.

Results: In this work, we focus on the question of clustering digital gene expression profiles as a means to discover groups of co-expressed genes. We propose a Poisson mixture model using a rigorous framework for parameter estimation as well as the choice of the appropriate number of clusters. We illustrate co-expression analyses using our approach on two real RNA-seq datasets. A set of simulation studies also compares the performance of the proposed model with that of several related approaches developed to cluster RNA-seq or serial analysis of gene expression data.

Availability: The proposed method is implemented in the open-source R package HTSCluster, available on CRAN.

drosophila_clusters

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