To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("flipflop")

In most cases, you don't need to download the package archive at all.

flipflop

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see flipflop.

Fast lasso-based isoform prediction as a flow problem

Bioconductor version: 3.1

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")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("flipflop")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("flipflop")

PDF	R Script	FlipFlop: Fast Lasso-based Isoform Prediction as a Flow Problem
PDF		Reference Manual
Text		NEWS

Details

biocViews	AlternativeSplicing, RNASeq, RNASeqData, Regression, Software
Version	1.6.1
In Bioconductor since	BioC 2.13 (R-3.0) (2.5 years)
License	GPL-3
Depends	R (>= 2.10.0)
Imports	methods, Matrix, IRanges, GenomicRanges, parallel
LinkingTo
Suggests	GenomicFeatures
SystemRequirements	GNU make
Enhances
URL	http://cbio.ensmp.fr/flipflop
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	flipflop_1.6.1.tar.gz
Windows Binary	flipflop_1.6.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	flipflop_1.6.1.tgz
Mac OS X 10.9 (Mavericks)	flipflop_1.6.1.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/flipflop/tree/release-3.1
Package Short Url	http://bioconductor.org/packages/flipflop/
Package Downloads Report	Download Stats

Documentation »

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