flipflop
This package is for version 3.8 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: 3.8
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>
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 | 1.20.0 |
| 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_1.20.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/flipflop/ |
| Package Short Url | https://bioconductor.org/packages/flipflop/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.8 | Source Archive |