Package: GenomicRanges Title: Representation and manipulation of genomic intervals and variables defined along a genome Description: The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages respectively. Both packages build on top of the GenomicRanges infrastructure. Version: 1.22.4 Encoding: UTF-8 Author: P. Aboyoun, H. Pagès, and M. Lawrence Maintainer: Bioconductor Package Maintainer biocViews: Genetics, Infrastructure, Sequencing, Annotation, Coverage, GenomeAnnotation Depends: R (>= 2.10), methods, BiocGenerics (>= 0.16.1), S4Vectors (>= 0.8.6), IRanges (>= 2.4.6), GenomeInfoDb (>= 1.1.20) Imports: utils, stats, XVector LinkingTo: S4Vectors, IRanges Suggests: Biobase, AnnotationDbi (>= 1.21.1), annotate, Biostrings (>= 2.25.3), Rsamtools (>= 1.13.53), SummarizedExperiment (>= 0.1.5), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq, DEXSeq, edgeR, KEGGgraph, BiocStyle, digest, RUnit, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2, KEGG.db, hgu95av2.db, org.Hs.eg.db, org.Mm.eg.db, org.Sc.sgd.db, pasilla, pasillaBamSubset, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 Collate: utils.R phicoef.R transcript-utils.R constraint.R strand-utils.R range-squeezers.R GenomicRanges-class.R GRanges-class.R DelegatingGenomicRanges-class.R GNCList-class.R GIntervalTree-class.R GenomicRanges-comparison.R GenomicRangesList-class.R GRangesList-class.R makeGRangesFromDataFrame.R SummarizedExperiment-class.R SummarizedExperiment-rowData-methods.R RangedData-methods.R intra-range-methods.R inter-range-methods.R coverage-methods.R setops-methods.R findOverlaps-methods.R findOverlaps-GIntervalTree-methods.R nearest-methods.R mapCoords-methods.R absoluteRanges.R tileGenome.R tile-methods.R genomicvars.R test_GenomicRanges_package.R zzz.R NeedsCompilation: yes Packaged: 2016-01-30 02:18:29 UTC; biocbuild Built: R 3.2.3; x86_64-pc-linux-gnu; 2016-10-26 17:39:57 UTC; unix