ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data.

ABSTRACT:

Background

Pathway analysis methods, in which differentially expressed genes are mapped to databases of reference pathways and relative enrichment is assessed, help investigators to propose biologically relevant hypotheses. The last generation of pathway analysis methods takes into account the topological structure of a pathway, which helps to increase both specificity and sensitivity of the findings. Simultaneously, the RNA-Seq technology is gaining popularity and becomes widely used for gene expression profiling. Unfortunately, majority of topological pathway analysis methods remains without implementation and if an implementation exists, it is limited in various factors.

Results

We developed a new R/Bioconductor package ToPASeq offering uniform interface to seven distinct

SUBMITTER: Ihnatova I 

PROVIDER: S-EPMC4625615 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature