The FLUX CAPACITOR specifications

Information

Unique identifier	OMICS_01293
Name	The FLUX CAPACITOR
Alternative name	Flux Simulator
Software type	Application/Script
Interface	Command line interface
Restrictions to use	None
Input data	An annotation of a reference transcriptome and reads fromRNAseq technologies aligned to the genome.
Input format	FASTA+GTF
Output data	Some reads and mappings
Output format	SAM
Operating system	Unix/Linux, Mac OS, Windows
Programming languages	Java
Computer skills	Advanced
Version	1.6.1
Stability	Stable
Maintained	Yes

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Documentation

Forum: http://sammeth.net/confluence/display/FLUX/Appendix+D+-+Forum

Maintainer

Michael Sammeth <>

Publications for The FLUX CAPACITOR

Modelling and simulating generic RNA-Seq experiments with the flux simulator.

2012 Nucleic Acids Res

PMCID: 3488205

PMID: 22962361

DOI: 10.1093/nar/gks666

Transcriptome genetics using second generation sequencing in a Caucasian population.

2010 Nature

PMCID: 3836232

PMID: 20220756

DOI: 10.1038/nature08903

The FLUX CAPACITOR IN pipeline

FCGR2C Polymorphisms Associated with HIV-1 Vaccine Protection Are Linked to Altered Gene Expression of Fc-γ Receptors in Human B Cells

2016

PMCID: 4807760

PMID: 27015273

DOI: 10.1371/journal.pone.0152425

[…] mrna quantification was calculated at different levels. for exon quantification, overlapping exons of a gene were first merged into meta-exons. transcripts and splice junctions were quantified by the flux capacitor approach [8]. gene quantification was calculated as the sum of all transcript rpkms (reads per kilobase per million) for each gene. before eqtl analysis, expression quantifications […]

The FLUX CAPACITOR institution(s)

Bioinformatics and Genomics Program, Centre de Regulacio Genomica (CRG), Barcelona, Spain; Functional Bioinformatics Group, Centre Nacional d’Analisi Genomica (CNAG), Barcelona; Computational Biology and Regulatory Networks Group, Gene Center Munich, Munich, Germany; Algorithm Development Group, Centre Nacional d’Analisi Genomica (CNAG), Barcelona, Spain; Statistical Genomics Group, Centre Nacional d’Analisi Genomica (CNAG), Barcelona, Spain; Biometrie et Biologie Evolutive, Universite Lyon 1, Villeurbanne, France

The FLUX CAPACITOR funding source(s)

Supported by the European Science Foundation, an Erasmus exchange grant of the European Community, a Post-doctoral fellowship of the Spanish Ministry of Science and Open Source license of Atlassian for their products Jira, Confluence and Fisheye and the Spanish Ministry of Science [BIO2006-03380 and CONSOLIDER CSD2007-00050].

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