GENE-counter

GENE-counter

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GENE-counter is a computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression of eukaryotes, prokaryotes, as well as organisms with no available genome reference sequence. GENE-counter is a complete pipeline that automates the process of enumerating, aligning, and assigning sequences to generate count data to simplify high-throughput sequence analysis. To analyze data for differential gene expression, GENE-counter can be run with any one of three statistics packages that are based on variations of the negative binomial distribution. The default method is a new and simple statistical test we developed based on an over-parameterized version of the negative binomial distribution. GENE-counter also includes three different methods for assessing differentially expressed features for enriched gene ontology (GO) terms.

Please reference: Cumbie JS, Kimbrel JA, Di Y, Schafer DW, Wilhelm LJ, et al. (2011) GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences. PLoS ONE 6(10): e25279. doi:10.1371/journal.pone.0025279

For more information concerning the statistical package developed for GENE-counter please see: Di, Yanming; Schafer, Daniel W.; Cumbie, Jason S.; and Chang, Jeff H. (2011) "The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq," Statistical Applications in Genetics and Molecular Biology: Vol. 10: Iss. 1, Article 24.