FunPat: function-based pattern analysis on RNA-seq time series data.

ABSTRACT:

Background

Dynamic expression data, nowadays obtained using high-throughput RNA sequencing, are essential to monitor transient gene expression changes and to study the dynamics of their transcriptional activity in the cell or response to stimuli. Several methods for data selection, clustering and functional analysis are available; however, these steps are usually performed independently, without exploiting and integrating the information derived from each step of the analysis.

Methods

Here we present FunPat, an R package for time series RNA sequencing data that integrates gene selection, clustering and functional annotation into a single framework. FunPat exploits functional annotations by performing for each functional term, e.g. a Gene Ontology term, an integrated selectio

SUBMITTER: Sanavia T 

PROVIDER: S-EPMC4460925 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature