GeneProf is a web-based, graphical software suite, designed to facilitate the analysis and interpretation of high-thoughput sequencing data. It allows users to analyse data produced using high-throughput sequencing platforms, downloaded from public repositories or from their own experiments.
At the moment, GeneProf focuses on RNA-seq transcriptomic data (gene expression, miRNAs, etc.) and ChIP-seq regulatory data (transcription factor binding, gene regulation, etc.) but ongoing work will expand GeneProf's scope further.
GeneProf can be used in two ways:
- As a resource for browsing, searching and visualising already analysed data from hundreds of studies;
- As an analysis tool to translate high-throughput sequencing data into biologically-meaningful results.
Some features include:
- Easy-to-use web-based interface: Access to data at any time, no need to install any software;
- Analysis wizards: Pre-defined, step-by-step workflows to analyse short read data;
- Versatile modules: Many advanced analysis modules available which can be combined freely;
- Integrated Analysis: Analysis of ChIP-seq and RNA-seq data in one place, as well as support for the integration of other external data (e.g. from microarrays);
- Comprehensive resource: Easy access and comparison to a set of expertly curated experimental results;
- Extensibility: Algorithm developers and computer programmers can develop their own modules and extend the functionality of GeneProf.
Public GeneProf data can be accessed through the web interface without registration. Users wishing to access their own data can register for a free account using the web interface. This account gives access to compute and some storage space for analysis results. Further storage is available upon request. GeneProf data is also available from a web services interface using a variety of popular languages. Examples of using this interface for Perl, Python, Java and R are provided on the GeneProf web site.