MOTIVATION: High-throughput screens (HTS) by RNAi or small molecules are among the most promising tools in functional genomics. They enable researchers to observe detailed reactions to experimental perturbations on a genome-wide scale. While there is a core set of computational approaches used in many publications to analyze these data, a specialized software combining them and making them easily accessible has so far been missing. RESULTS: Here we describe HTSanalyzeR, a flexible software to build integrated analysis pipelines for HTS data that contains over-representation analysis, gene set enrichment analysis, comparative gene set analysis and rich sub-network identification. HTSanalyzeR interfaces with commonly used pre-processing packages for HTS data and presents its results as HTML pages and network plots. AVAILABILITY: Our software is written in the R language and freely available via the Bioconductor project at http://www.bioconductor.org.