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Protocols

The FLUX CAPACITOR specifications

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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 No

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Publications for The FLUX CAPACITOR

The FLUX CAPACITOR citations

 (7)
library_books

The lipid sensor GPR120 promotes brown fat activation and FGF21 release from adipocytes

2016
Nat Commun
PMCID: 5118546
PMID: 27853148
DOI: 10.1038/ncomms13479

[…] sion 2.02 (ref. ) under default options for paired-end read mapping. Mapped reads were used to quantify transcripts from the Ensembl version 73 gene annotation data set (http://www.ensembl.org) using the Flux Capacitor approach. This strategy deconvolutes reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations, and thus specifically assigns some re […]

library_books

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

2016
PLoS One
PMCID: 4807760
PMID: 27015273
DOI: 10.1371/journal.pone.0152425

[…] the 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 []. Gene quantification was calculated as the sum of all transcript RPKMs (reads per kilobase per million) for each gene. Before eQTL analysis, expression quantifications w […]

library_books

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes

2016
Genome Biol
PMCID: 4766624
PMID: 26911872
DOI: 10.1186/s13059-016-0883-6

[…] etermined applying the procedure described above for homology-based prediction to the 12 plant genomes using all bean transcript models as templates. lncRNA transcript expressions were obtained using the Flux Capacitor []. […]

library_books

Analysis artefacts of the INS IGF2 fusion transcript

2015
BMC Mol Biol
PMCID: 4517550
PMID: 26220792
DOI: 10.1186/s12867-015-0042-8

[…] tly, it should be mentioned that several recent publications of islet transcriptomics data do not report on a faulty INS-IGF2 expression as they specifically handle this issue. Eizirik et al. [] used the Flux Capacitor approach [] to specifically handle the problem of reads mapping to exonic regions shared by multiple transcripts. Moran et al. [] addressed the multiple transcript mapping issue by […]

call_split

Nova1 is a master regulator of alternative splicing in pancreatic beta cells

2014
Nucleic Acids Res
PMCID: 4191425
PMID: 25249621
DOI: 10.1093/nar/gku861
call_split See protocol

[…] database () version 70 for transcripts assembly using the novel transcripts discovery options. Transcript quantification from the mapped reads and the newly assembled transcripts was performed using the Flux Capacitor approach developed by one of us (M.S.) (http://flux. sammeth.net, ()). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units (‘reads per ki […]

library_books

Modeling gene expression using chromatin features in various cellular contexts

2012
Genome Biol
PMCID: 3491397
PMID: 22950368
DOI: 10.1186/gb-2012-13-9-r53

[…] number of mapped RNA-PET 5' tags in the experiment. For RNA-Seq experiments, we used GENCODE v7 transcript expression as measured by RPKM (reads per kilobase per million mapped reads; computed using the flux capacitor []) to measure GENCODE v7 TSS expression. If a TSS is shared by transcripts t1,... tn, its expression in an RNA-Seq experiment will be defined as the sum of the RPKM of transcripts […]


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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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