DOI: 10.18129/B9.bioc.flipflop    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of flipflop; to use it, please install the devel version of Bioconductor.

Fast lasso-based isoform prediction as a flow problem

Bioconductor version: Development (3.10)

Flipflop discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data. It takes an alignment file in SAM format as input. It can also discover transcripts from several samples simultaneously, increasing statistical power.

Author: Elsa Bernard, Laurent Jacob, Julien Mairal and Jean-Philippe Vert

Maintainer: Elsa Bernard <elsa.bernard at mines-paristech.fr>

Citation (from within R, enter citation("flipflop")):


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


PDF   Reference Manual


biocViews AlternativeSplicing, RNASeq, RNASeqData, Regression, Software
Version 1.23.1
In Bioconductor since BioC 2.13 (R-3.0) (5.5 years)
License GPL-3
Depends R (>= 2.10.0)
Imports methods, Matrix, IRanges, GenomicRanges, parallel
Suggests GenomicFeatures
SystemRequirements GNU make
URL http://cbio.ensmp.fr/flipflop
Depends On Me
Imports Me
Suggests Me
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Source Package
Windows Binary flipflop_1.23.1.zip
Mac OS X 10.11 (El Capitan)
Source Repository git clone https://git.bioconductor.org/packages/flipflop
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/flipflop
Package Short Url http://bioconductor.org/packages/flipflop/
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