flipflop

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

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	1.20.0
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
LinkingTo
Suggests	GenomicFeatures
SystemRequirements	GNU make
Enhances
URL	http://cbio.ensmp.fr/flipflop
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	flipflop_1.20.0.tar.gz
Windows Binary	flipflop_1.20.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	flipflop_1.20.0.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	http://bioconductor.org/packages/flipflop/
Package Downloads Report	Download Stats