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web cellHTS2: a web-application for the analysis of high-throughput screening data.

Oliver Pelz1, Moritz Gilsdorf, Michael Boutros

  • 1German Cancer Research Center (DKFZ), Div Signaling and Functional Genomics and University of Heidelberg, Faculty of Medicine Mannheim, Dept Cell and Molecular Biology, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany.

BMC Bioinformatics
|April 14, 2010
PubMed
Summary

This study introduces web cellHTS2, a user-friendly web application for analyzing large RNAi screening datasets. It streamlines the identification of phenotypic hits in high-throughput biological experiments.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • High-throughput screening (HTS) generates large datasets for biological discovery.
  • RNA interference (RNAi) screens are crucial for identifying factors influencing cellular processes.
  • Analysis and annotation of HTS data are essential for identifying phenotypic hits.

Purpose of the Study:

  • To present a web-based application for end-to-end analysis of large cell-based screening experiments.
  • To provide a user-friendly interface for analyzing high-throughput screening data.
  • To facilitate the identification of novel factors in cellular processes.

Main Methods:

  • Development of a web application, web cellHTS2, for HTS data analysis.
  • Integration with the cellHTS2 R/Bioconductor package via an R-server for parallel processing.

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  • Implementation of options for data standardization, normalization, and annotation.
  • Provision of file import and configuration modules for common formats.

    • Main Results:

    • The software guides users through single or multi-channel experiment analysis.
    • Comprehensive HTML reports with ranked hit lists are generated.
    • Sessions can be saved and restored for re-analysis.
    • Highly parallel analysis of screening datasets is enabled.

    Conclusions:

    • web cellHTS2 facilitates high-throughput data analysis with a user-friendly interface.
    • The application is accessible online and offers downloadable standalone versions.
    • web cellHTS2 is freely distributed under the GPL license.