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Old 01-30-2012, 02:21 AM   #1
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Location: Edinburgh, UK

Join Date: Nov 2008
Posts: 7
Arrow GeneProf - Next-Gen Analysis for Next-Gen Data

Hi all,

I'm delighted to announce the release of GeneProf, a new data analysis suite for high-throughput sequencing data from RNA-seq and ChIP-seq experiments. GeneProf aims to simplify common data processing tasks (quality control, alignment, gene expression analysis, peak calling), in particular, but not only, for novice data analysts and experimental biologists. In addition, GeneProf provides a resource of ready-analysed HTS experiments with transparent and reproducible analysis pipelines.

Some of GeneProf's highlights include:

* Easy-to-use web-based interface: Access your data at any time from any reasonably modern computer with a working internet connection -- no need to install any software!
* Analysis wizards make your life easy: Pre-defined, step-by-step workflows make it possible for anybody to analyse their short read data in a minimum of hands-on time.
* Versatile modules: Advanced users and data analysis experts benefit from GeneProf's broad range of analysis modules, which can be combined freely in a dynamic workflow environment.
* Integrated Analysis: Analysis ofChIP-seq and RNA-seq data in one place, plus support for the integration of other external data (e.g. from microarrays).
* Comprehensive Resource: GeneProf provides a comprehensive resource of analysed next-generation sequencing data. Experimental results can be easily accessed and compared and the analysis procedures employed to produce the data are fully transparent and can be accessed readily.
* Extensibility: Algorithm developers and computer programmers can develop their own modules and extend the functionality of GeneProf. Existing software can be easily wrapped and integrated in the GeneProf framework (N.B. this part is a bit rough and not sufficiently documented at the moment, but will be improved in future!)
* Web API: Data from GeneProf may be used externally via a web-accessible API.

A public instance of GeneProf is freely accessible by academic researchers at:

We are currently waiting for our host institution to sort out some legal stuff and once they give their OK, you will also be able to download the software for local installation and obtain source code for all data analysis components.

For further information, please refer to the associated publication (or get in touch!):
Halbritter F, Vaidya HJ, Tomlinson SR. GeneProf: analysis of high-throughput sequencing experiments. Nature Methods 9(1), 7-8 (2011). PubMed ID: 22205509

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