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HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens

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 ma...

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Detalles Bibliográficos
Autores principales: Wang, Xin, Terfve, Camille, Rose, John C., Markowetz, Florian
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051329/
https://www.ncbi.nlm.nih.gov/pubmed/21258062
http://dx.doi.org/10.1093/bioinformatics/btr028
Descripción
Sumario: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. Contact: florian.markowetz@cancer.org.uk