HTSanalyzeR

Functional genomics has demonstrated considerable success in inferring the inner working of a cell through analysis of its response to various perturbations. In recent years several technological advances have pushed high-throughput screens (HTS) to the forefront of functional genomics.

Features

The software package HTSanalyzeR provides state-of-the-art analysis methods for HTS in a unified framework. Features of the current release (which is under review at Bioconductor) include:

• Bioconductor compliant R package
• Works hand in hand with cellHTS2, the leading package for pre-processing of cell-based high-throughput screens.
• Output as HTML pages in easy to interpret list and figures.
• Gene set and pathway analysis
• based on gene sets defined in MSigDB and Gene Ontology
• Overrepresentation analysis of hits based on hyper-geometric distribution
• Cutoff free Gene Set Enrichment Analysis
• Network enrichment analysis
• Interface to BioGRID database
• Identifies rich subnetworks using the BioNet algorithm

Download

You can download the latest version from here

References

• HTSanalyzeR: an R/Bioconductor package for network analysis of high throughput screens
  John C. Rose, Camille D.A. Terfve and Florian Markowetz (in preparation), 2010
• How to understand the cell by breaking it: network analysis of gene perturbation screens
  F. Markowetz, PLoS Comp Bio, 2010 Feb 26;6(2):e1000655.
  [ PMID:20195495 | doi:10.1371/journal.pcbi.1000655 | arXiv:0910.2938 ]