GeneProf
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Application data |
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| Created by | Halbritter F, Tomlinson SR |
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| Biological application domain(s) | Functional Genomics, RNA-Seq, ChIP-Seq |
| Principal bioinformatics method(s) | Workflow, Quality Control, Alignment, Visualization, Peak finding, Differentially expressed gene identification |
| Technology | Illumina |
| Created at | University of Edinburgh |
| Maintained? | Yes |
| Input format(s) | FASTA, FASTA, (Compressed) FASTA, (Compressed) FASTQ, Tab-delimited, Table with count data, Others |
| Output format(s) | Various image file formats, XLS, TXT, FASTA, FASTQ, BED, WIG, Tab-delimited, HTML, R |
| Software features | User-friendly, wizards, tutorials, examples, very flexible, reproducible, transparent, extensible, API |
| Programming language(s) | Java, Javascript |
| Software libraries | many |
| Licence | Free for academic use |
| Operating system(s) | webserver (any) |
Summary: GeneProf is a web-based, graphical software suite and database resource for high-throughput-sequencing experiments (RNA-seq and ChIP-seq).
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Description
GeneProf is a web-based, graphical software suite that allows users to analyse data produced using high-throughput sequencing platforms (RNA-seq and ChIP-seq): Next-gen analysis for next-gen data!
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 graphical workflows.
- Integrated Analysis: Analysis of ChIP-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 analyzed 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 and data from GeneProf may be used externally.
GeneProf is academic software developed at the Centre for Regenerative Medicine / Institute for Stem Cell Research, University of Edinburgh and has benefited from funding by the Medical Research Council and the EU Framework 7 Project "EuroSyStem".
Links
References
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| Web Search | Wiki Sites | Scientific |
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