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# Configuration file defining R specific libraries that are installed
# via CRAN and Bioconductor.
cranrepo: http://cran.fhcrc.org/
cran:
- abind
- ape
- aplpack
- biglm
- BiodiversityR
- bitops
- boot
- car
- caret
- caTools
- chron
- class
- cluster
- codetools
- coin
- colorspace
- date
- DBI
- devtools
- digest
- effects
- FactoMineR
- flashClust
- foreign
- gdata
- gee
- graph
- ggplot2
- gplots
- gsalib
- gtools
- hdf5
- hexbin
- hmisc
- HH
- hwriter
- kernlab
- kernsmooth
- knitr
- lattice
- latticeExtra
- leaps
- lmtest
- maptree
- markdown
- mass
- matrix
- mclust
- mgcv
- modeltools
- multcomp
- multicore
- nlme
- NMF
- nnet
- pamr
- pi0
- plotrix
- plyr
- proto
- qvalue
- rcmdr
- relimp
- reshape
- reshape2
- rgl
- RColorBrewer
- RCurl
- rpart
- rjson
- Rmpi
- RMySQL
- RSQLite
- sandwich
- sm
- snowfall
- spatial
- sqldf
- statmod
- stringr
- strucchange
- survival
- testthat
- vegan
- vgam
- VennDiagram
- vr
- XML
- xtable
- yacca
- yaml
- zoo
biocrepo: http://bioconductor.org/biocLite.R
bioc:
- affxparser
- affy
- affydata
- affyio
- affyPLM
- affyQCReport
- annaffy
- annotate
- AnnotationDbi
- aroma.light
- ArrayExpress
- arrayQualityMetrics
- ArrayTools
- BayesPeak
- baySeq
- beadarray
- Biobase
- BiocInstaller
- bioDist
- biomaRt
- Biostrings
- BSgenome
#- BSgenome.Athaliana.TAIR.TAIR9
#- BSgenome.Celegans.UCSC.ce6
#- BSgenome.Dmelanogaster.UCSC.dm3
#- BSgenome.Hsapiens.UCSC.hg19
#- BSgenome.Mmusculus.UCSC.mm9
#- BSgenome.Scerevisiae.UCSC.sacCer3
- ChIPpeakAnno
- chipseq
- ChIPseqR
- ChIPsim
- CNAnorm
- cn.mops
- CSAR
- cummeRbund
- DEGseq
- DESeq
- DEXSeq
- DiffBind
- DNAcopy
- DynDoc
- edgeR
- EDASeq
- exomeCopy
- gage
- gcrma
- genefilter
- geneplotter
- GenomeGraphs
- genomeIntervals
- GenomicFeatures
- GenomicRanges
- Genominator
- GEOquery
- GGBase
- GGtools
- ggbio
- girafe
- globaltest
#- GO.db
- GOFunction
- goseq
- GOstats
- GSEABase
- GWASTools
- hgu95av2.db
- HilbertVis
- htSeqTools
- impute
- IRanges
- KEGG.db
- limma
- lumi
- makecdfenv
- marray
- MEDIPS
- multtest
- MotIV
- mzR
- oneChannelGUI
#- org.At.tair.db
#- org.Ce.eg.db
#- org.Dm.eg.db
#- org.Hs.eg.db
#- org.Mm.eg.db
#- org.Sc.sgd.db
#- org.Xl.eg.db
- PAnnBuilder
- preprocessCore
- PICS
- qpgraph
- qrqc
- rGADEM
- R453Plus1Toolbox
- RBGL
- Repitools
- rGADEM
- Rgraphviz
- Ringo
- rnaSeqMap
- Rolexa
- Rsamtools
- Rsubread
- rtracklayer
- segmentSeq
- seqbias
- seqLogo
- ShortRead
- siggenes
- simpleaffy
- snpMatrix
- snpStats
- splots
- SRAdb
- tkWidgets
- VariantAnnotation
- vsn
- widgetTools
- xcms
- zlibbioc