The FLUX CAPACITOR protocols

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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 No

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Publications for The FLUX CAPACITOR

The FLUX CAPACITOR in pipelines

 (3)
2016
PMCID: 4766624
PMID: 26911872
DOI: 10.1186/s13059-016-0883-6

[…] 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 []., small non-coding rnas were predicted using the cmsearch tool from the infernal package (v.1.1rc2) []. an e-value cutoff of 0.01 allowed detection of 2529 non-overlapping hits; […]

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 []. gene quantification was calculated as the sum of all transcript rpkms (reads per kilobase per million) for each gene. before eqtl analysis, expression quantifications […]

2014
PMCID: 4191425
PMID: 25249621
DOI: 10.1093/nar/gku861

[…] 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 […]


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The FLUX CAPACITOR in publications

 (6)
PMCID: 5118546
PMID: 27853148
DOI: 10.1038/ncomms13479

[…] 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 […]

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 []. gene quantification was calculated as the sum of all transcript rpkms (reads per kilobase per million) for each gene. before eqtl analysis, expression quantifications […]

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

[…] 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 []., small non-coding rnas were predicted using the cmsearch tool from the infernal package (v.1.1rc2) []. an e-value cutoff of 0.01 allowed detection of 2529 non-overlapping hits; […]

PMCID: 4826667
PMID: 27110296
DOI: 10.1007/s12559-015-9366-4

[…] with further crowd-sourcing studies., the creative generation of characters for stories has also been explored in the context of fictional ideation. examples of this are the party quirks [] and the flux capacitor [] systems. the former is a digital improvisational theatre game that allows the generation of imaginary characters by manipulating their stereotypical attributes, e.g. a clumsy […]

PMCID: 4517550
PMID: 26220792
DOI: 10.1186/s12867-015-0042-8

[…] 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 […]


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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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