flipflop

This package is for version 3.7 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see flipflop.

Fast lasso-based isoform prediction as a flow problem


Bioconductor version: 3.7

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 (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("flipflop")

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

Documentation

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

browseVignettes("flipflop")
FlipFlop: Fast Lasso-based Isoform Prediction as a Flow Problem PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews AlternativeSplicing, RNASeq, RNASeqData, Regression, Software
Version 1.18.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License GPL-3
Depends R (>= 2.10.0)
Imports methods, Matrix, IRanges, GenomicRanges, parallel
System Requirements GNU make
URL http://cbio.ensmp.fr/flipflop
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Package Archives

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

Source Package flipflop_1.18.0.tar.gz
Windows Binary flipflop_1.18.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) flipflop_1.18.0.tgz
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 https://bioconductor.org/packages/flipflop/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive