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("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 | R Script | |
Reference Manual | ||
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 |
See More
Suggests | GenomicFeatures |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
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 |