chimera

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 chimera.

A package for secondary analysis of fusion products


Bioconductor version: 3.7

This package facilitates the characterisation of fusion products events. It allows to import fusion data results from the following fusion finders: chimeraScan, bellerophontes, deFuse, FusionFinder, FusionHunter, mapSplice, tophat-fusion, FusionMap, STAR, Rsubread, fusionCatcher.

Author: Raffaele A Calogero, Matteo Carrara, Marco Beccuti, Francesca Cordero

Maintainer: Raffaele A Calogero <raffaele.calogero at unito.it>

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

Installation

To install this package, start R (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("chimera")

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("chimera")
chimera PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Infrastructure, Software
Version 1.22.0
In Bioconductor since BioC 2.12 (R-3.0) (11 years)
License Artistic-2.0
Depends Biobase, GenomicRanges(>= 1.13.3), Rsamtools(>= 1.13.1), GenomicAlignments, methods, AnnotationDbi, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, Homo.sapiens
Imports
System Requirements STAR, TopHat, bowtie and samtools are required for some functionalities
URL
See More
Suggests BiocParallel, geneplotter
Linking To
Enhances Rsubread, BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene
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 chimera_1.22.0.tar.gz
Windows Binary chimera_1.22.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) chimera_1.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/chimera
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/chimera
Package Short Url https://bioconductor.org/packages/chimera/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive