DOI: 10.18129/B9.bioc.flipflop    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see flipflop.

Fast lasso-based isoform prediction as a flow problem

Bioconductor version: 3.8

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")):


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PDF R Script FlipFlop: Fast Lasso-based Isoform Prediction as a Flow Problem
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biocViews AlternativeSplicing, RNASeq, RNASeqData, Regression, Software
Version 1.20.0
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
Links To Me
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Source Package flipflop_1.20.0.tar.gz
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Package Short Url http://bioconductor.org/packages/flipflop/
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