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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("chimera")
In most cases, you don't need to download the package archive at all.
chimera
A package for secondary analysis of fusion products
Bioconductor version: 3.0
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, tophat-fusion-post, 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 and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("chimera")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("chimera")
| R Script | chimera | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Infrastructure, Software |
| Version | 1.8.5 |
| In Bioconductor since | BioC 2.12 (R-3.0) |
| License | Artistic-2.0 |
| Depends | Biobase, GenomicRanges(>= 1.13.3), Rsamtools(>= 1.13.1), GenomicAlignments, methods, AnnotationDbi, org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene |
| Imports | |
| LinkingTo | |
| Suggests | BiocParallel, Rbowtie, geneplotter |
| SystemRequirements | STAR, TopHat, bowtie and samtools are required for some functionalities |
| Enhances | Rsubread, BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db |
| URL | |
| Depends On Me | oneChannelGUI |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | chimera_1.8.5.tar.gz |
| Windows Binary | chimera_1.8.5.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | chimera_1.8.5.tgz |
| Mac OS X 10.9 (Mavericks) | chimera_1.8.5.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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