flipflop

DOI: 10.18129/B9.bioc.flipflop    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see flipflop.

Fast lasso-based isoform prediction as a flow problem

Bioconductor version: 3.9

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 "3.6") 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

PDF		Reference Manual

Details

biocViews	AlternativeSplicing, RNASeq, RNASeqData, Regression, Software
Version	1.22.0
In Bioconductor since	BioC 2.13 (R-3.0) (6 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
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Build Report

Package Archives

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

Source Package
Windows Binary	flipflop_1.22.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	flipflop_1.21.0.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