Last data update: 2014.03.03
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chimera
Package: chimera
Type: Package
Title: A package for secondary analysis of fusion products
Version: 1.14.0
Date: 31 March 2015
Author: Raffaele A Calogero, Matteo Carrara, Marco Beccuti, Francesca Cordero
Maintainer: Raffaele A Calogero <raffaele.calogero@unito.it>
Depends: Biobase, GenomicRanges (>= 1.13.3), Rsamtools (>= 1.13.1),
GenomicAlignments, methods, AnnotationDbi,
BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene,
Homo.sapiens
Suggests: BiocParallel, geneplotter
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
Description: 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.
biocViews: Infrastructure
SystemRequirements: STAR, TopHat, bowtie and samtools are required for
some functionalities
License: Artistic-2.0
NeedsCompilation: yes
Packaged: 2016-05-04 04:52:34 UTC; biocbuild
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'chimera' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c StarParser.cpp -o StarParser.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o chimera.so StarParser.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/chimera/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'chimera'
finding HTML links ... done
MHmakeRandomString html
bam2fastq html
breakpointOverlaps html
chimera-package html
chimeraSeqSet html
chimeraSeqs html
class.fSet html
defuseTPTN html
filterList html
filterSamReads html
fusionName html
fusionPeptides html
gapfillerInstallation html
gapfillerRun html
gapfillerWrap html
importFusionData html
is.fSet html
newfSet html
oncofuseInstallation html
oncofuseRun html
picardInstallation html
plotCoverage html
prettyPrint html
removingErrorLine html
starInstallation html
starReads html
starRun html
subreadRun html
supportingReads html
tophatInstallation html
tophatRun html
validateSamFile html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (chimera)
Making 'packages.html' ... done
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