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
- 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 ]