chimera

DOI: 10.18129/B9.bioc.chimera    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.12 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: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

PDF	R Script	chimera
PDF		Reference Manual
Text		NEWS

Details

biocViews	Infrastructure, Software
Version	1.32.0
In Bioconductor since	BioC 2.12 (R-3.0) (8 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
LinkingTo
Suggests	BiocParallel, geneplotter
SystemRequirements	STAR, TopHat, bowtie and samtools are required for some functionalities
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
URL
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	chimera_1.32.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)	chimera_1.32.0.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