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Interpretation of RNAi screens requires computational and statistical analysis techniques. We describe a method that integrates all steps to generate a scored phenotype list from raw data. It is implemented in an open-source Bioconductor\/R package, <jats:italic>cellHTS<\/jats:italic> (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.dkfz.de\/signaling\/cellHTS\">http:\/\/www.dkfz.de\/signaling\/cellHTS<\/jats:ext-link>). The method is useful for the analysis and documentation of individual RNAi screens. 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