Table 1. Examples of software for network analysis of gene perturbation screens.
| Method Name | Description with Reference | Web Page |
| General data analysis and network visualization | ||
| Bioconductor | Software environment for the analysis of genomic data featuring hundreds of contributed packages [112] | www.bioconductor.org |
| Cytoscape | Software platform for visualizing molecular interaction networks and integrating them with other data types [113] | www.cytoscape.org |
| Setting up data for network analysis | ||
| cellHTS2 | End-to-end analysis of cell-based screens: from raw intensity readings to the annotated hit list [6] | www.bioconductor.org |
| RNAither | Analysis of cell-based RNAi screens, includes quality assessment and customizable normalization [7] | www.bioconductor.org |
| EBImage | Cell image analysis and feature extraction [27] | www.bioconductor.org |
| CellProfiler | Cell image analysis and feature extraction [26] | www.cellprofiler.org |
| Enrichment analysis | ||
| DAVID | Tools for data annotation, visualization, and integration [36] | david.abcc.ncifcrf.gov |
| GOLEM | Enrichment analysis and visualization of GO graph (Figure 2A) [37] | function.princeton.edu/GOLEM |
| Ontologizer | Enrichment analysis with dependencies between GO nodes (Figure 2A) [38] | compbio.charite.de/ontologizer |
| GSEA | Gene set enrichment analysis (Figure 2B) [35] | www.broadinstitute.org/gsea/ |
| Clustering and ranking | ||
| Cell Profiler Analyst | Interactive exploration and analysis of multidimensional data from image-based experiments [28] | www.cellprofiler.org |
| PhenoBlast | Ranking of phenotype profiles according to similarity with given profile [11] | www.rnai.org |
| Endeavour | Prioritizes hits for further analysis [58] | www.esat.kuleuven.be/endeavour/ |
| Finding rich subnetworks | ||
| heinz | Finds optimal subnetworks rich in hits (Figure 3A) [55] | www.planet-lisa.net |
| jActiveModules | Finds heuristic subnetworks rich in hits (Figure 3A) [53] | www.cytoscape.org |
| Matisse | Finds subnetworks with high phenotypic similarity (Figure 3B) [74] | acgt.cs.tau.ac.il/matisse/ |
| Network reconstruction | ||
| nem | NEMs reconstruct pathway features from subset relations in high-dim phenotypes [90] | www.bioconductor.org |
| copia | Copia uses MIMO models to reconstruct networks from perturbations [84] | cbio.mskcc.org/copia/ |
This list is far from comprehensive, but hopefully provides a starting point even for noncoding experimentalists.