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FlipFlop specifications


Unique identifier OMICS_04028
Name FlipFlop
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data An alignment file
Input format SAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.18.0
Stability Stable
R(>=2.10.0), methods, parallel, IRanges, GenomicRanges, Matrix, GenomicFeatures
Maintained Yes


No version available



  • person_outline Elsa Bernard

Publications for FlipFlop

FlipFlop citations


The flipflop orphan genes are required for limb bud eversion in the Tribolium embryo

Front Zool
PMCID: 5649079
PMID: 29075305
DOI: 10.1186/s12983-017-0234-9

[…] In wildtype Tribolium larvae, appendages develop as everted structures outside the larval body (Fig. ). The RNAi mediated knockdown of the gene Tc-flipflop1 (Tc-ff1) results in an enigmatic novel RNAi cuticle phenotype where larval appendages developed inside the larval body (outside-in phenotype). This gene was uncovered during the iBeetle pres […]


Evaluating approaches to find exon chains based on long reads

Brief Bioinform
PMCID: 5952954
PMID: 28069635
DOI: 10.1093/bib/bbw137

[…] ented the concepts proposed by Rizzi et al. in the transcript prediction tool Traphlor, and using simulated data demonstrated against two state-of-the-art transcript prediction tools StringTie [] and FlipFlop [] that using the information provided by exon chains can significantly improve the transcript prediction accuracy.However, with the high error rates of the third-generation sequencers (∼15% […]


Benchmark analysis of algorithms for determining and quantifying full length mRNA splice forms from RNA seq data

PMCID: 4673975
PMID: 26338770
DOI: 10.1093/bioinformatics/btv488

[…] o from short read RNA-Seq data, of which Cufflinks () is the most widely used. Other methods are StringTie (), Scripture (), Trinity (), Oases (Velvet) (), Soap-denovo-trans (), iReckon (), CLASS (), FlipFlop (), IsoLasso (), MiTie (), Trans-ABySS (), AUGUSTUS (), Traph ().Algorithms are classified by whether they use an alignment to a reference genome sequence, or whether they assemble the reads […]


Interactive Pharmacometric Applications Using R and the Shiny Package

PMCID: 4394611
PMID: 26225240
DOI: 10.1002/psp4.21

[…] running the applications locally using R or by means of the Internet. They can be accessed at the following Web addresses: Flip-Flop Kinetics Application (Example 1): https://acp-unisa.shinyapps.io/FlipFlop/ Preliminary Patient Education Tool Application (Example 2): https://acp-unisa.shinyapps.io/OpenDay/ Ibuprofen in Pre-Term Neonates Application (Example 3): https://acp-unisa.shinyapps. […]


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FlipFlop institution(s)
Mines ParisTech, Centre for Computational Biology, Fontainebleau, France; Institut Curie, Paris, France; INSERM U900, Paris, France; Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France; LEAR Project-Team, INRIA Grenoble Rhône Alpes, Montbonnot, France

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