flipflop

DOI: 10.18129/B9.bioc.flipflop    

This is the development version of flipflop; for the stable release version, see flipflop.

Fast lasso-based isoform prediction as a flow problem

Bioconductor version: Development (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>

Citation (from within R, enter citation("flipflop")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("flipflop", version = "3.9")

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

Documentation

PDF   Reference Manual

Details

biocViews AlternativeSplicing, RNASeq, RNASeqData, Regression, Software
Version 1.21.0
In Bioconductor since BioC 2.13 (R-3.0) (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
Windows Binary flipflop_1.21.0.zip
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 http://bioconductor.org/packages/flipflop/
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