GENE-Counter
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Application data |
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| Created by | Jason Cumbie |
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| Biological application domain(s) | RNA-Seq |
| Created at | Oregon State University |
| Maintained? | Yes |
| Input format(s) | FASTA |
| Operating system(s) | Linux, Mac OS X |
Summary: GENE-counter is a computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression
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Description
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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References
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