This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see flipflop.
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 (from within R,
enter citation("flipflop")
):
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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("flipflop")
R Script | FlipFlop: Fast Lasso-based Isoform Prediction as a Flow Problem | |
Reference Manual | ||
Text | NEWS |
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 |
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 |
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