RSeqNP: A non-parametric approach for detecting differential expression and splicing from RNA-Seq data

Abstract

Summary: High-throughput sequencing of transcriptomes (RNA-Seq) has become a powerful tool to study gene expression. Here we present an R package, rSeqNP, which implements a non-parametric approach to test for differential expression and splicing from RNA-Seq data. rSeqNP uses permutation tests to access statistical significance and can be applied to a variety of experimental designs. By combining information across isoforms, rSeqNP is able to detect more differentially expressed or spliced genes from RNA-Seq data. Availability and implementation: The R package with its source code and documentation are freely available at http://www-personal.umich.edu/∼jianghui/rseqnp/.