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FX | An RNA-Seq analysis tool on the cloud

Allows RNA-Seq data analysis. FX permits to start immediately the process upon completion of sequencing. It provides the following steps: (1) pre-processing, (2) mapping on cDNA sequences, (3) bioinformatic filter conditions, (4) profiling of transcript expression. It employs a concept of bases per kilobase of gene model per million mapped bases (BPKM) to normalize the expression level of each gene.

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FX forum

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FX classification

FX specifications

Unique identifier:
OMICS_01403
Software type:
Framework/Library
Restrictions to use:
None
Operating system:
Unix/Linux
Computer skills:
Advanced
High performance computing:
Yes
Name:
user-Friendly gene eXpression analytic tool
Interface:
Command line interface
Output data:
Some gene expression profiles, SNP calls and short indels.
Parallelization:
MapReduce
Maintained:
No

FX distribution

versioning

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No open topic.

FX classification

FX specifications

Unique identifier:
OMICS_01403
Interface:
Web user interface
Computer skills:
Basic
Name:
user-Friendly gene eXpression analytic tool
Restrictions to use:
None
Maintained:
No

FX support

Maintainer

This tool is not available anymore.

Credits

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Publications

Institution(s)

Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, South Korea; Cancer Genomics Branch and Research Institute and Hospital, National Cancer Center, Goyang, South Korea; Department of Computer Science and Engineering, Ewha Womans University, Seoul, South Korea; Department of Biochemistry, Seoul National University College of Medicine, Seoul, South Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea; Psoma Therapeutics Inc., Seoul, South Korea; Macrogen Inc., Seoul, South Korea; Axeq Technologies, Rockville, MD, USA

Funding source(s)

Supported by Green Cross Therapeutics (grant No. 0411-20080023); Korean Ministry of Knowledge Economy (grant No. 10037410-2011-02); Korean Ministry of Education, Science, Technology (grant No. M10305030000; grant No. 2010-0013662); Small Medium Business Administration (grant No. 000358780109); Amazon Web Services (June 2011 EDU research award) in part.

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.