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Short description:
Please summarise the application in a few sentences. Avoid links here. GENE-counter is a computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
RNA-Seq,
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
Oregon State University,
== Description == <!-- Describe the application in the space below --> 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. <!-- -->
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