Package: oligo
Version: 1.71.7
Title: Preprocessing tools for oligonucleotide arrays
Author: Benilton Carvalho and Rafael Irizarry
Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Maintainer: Benilton Carvalho <benilton@unicamp.br>
Depends: R (>= 3.2.0),
         BiocGenerics (>= 0.13.11),
         oligoClasses (>= 1.29.6),
         Biobase (>= 2.27.3),
         Biostrings (>= 2.35.12)
Imports: affyio (>= 1.35.0),
         affxparser (>= 1.39.4),
         DBI (>= 0.3.1),
         ff,
         graphics,
         methods,
         preprocessCore (>= 1.29.0),
         RSQLite (>= 1.0.0),
         splines,
         stats,
         stats4,
         utils,
         bit
Enhances: doMC,
          doMPI
LinkingTo: preprocessCore
Suggests: BSgenome.Hsapiens.UCSC.hg18,
          hapmap100kxba,
          pd.hg.u95av2,
          pd.mapping50k.xba240,
          pd.huex.1.0.st.v2,
          pd.hg18.60mer.expr,
          pd.hugene.1.0.st.v1,
          maqcExpression4plex,
          genefilter,
          limma,
          RColorBrewer,
          oligoData,
          BiocStyle, knitr,
          RUnit,
          biomaRt,
          AnnotationDbi,
          ACME,
          RCurl
VignetteBuilder: knitr
Description: A package to analyze oligonucleotide arrays
        (expression/SNP/tiling/exon) at probe-level. It currently
        supports Affymetrix (CEL files) and NimbleGen arrays (XYS
        files).
License: LGPL (>= 2)
Collate: AllGenerics.R
         methods-GenericArrays.R
         methods-GeneFeatureSet.R
         methods-ExonFeatureSet.R
         methods-ExpressionFeatureSet.R
         methods-ExpressionSet.R
         methods-LDS.R
         methods-FeatureSet.R
         methods-SnpFeatureSet.R
         methods-SnpCnvFeatureSet.R
         methods-TilingFeatureSet.R
         methods-HtaFeatureSet.R
         methods-DBPDInfo.R
         methods-background.R
         methods-normalization.R
         methods-summarization.R
         read.celfiles.R
         read.xysfiles.R
         utils-general.R
         utils-selectors.R
         todo-snp.R
         functions-crlmm.R
         functions-snprma.R
         justSNPRMA.R
         justCRLMM.R
         methods-snp6.R
         methods-genotype.R
         methods-PLMset.R
         zzz.R
LazyLoad: Yes
URL: https://github.com/benilton/oligo
biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP,
        DifferentialExpression, ExonArray, GeneExpression, DataImport