Package: contiBAIT
Type: Package
Title: Improves Early Build Genome Assemblies using Strand-Seq Data
Version: 1.4.0
Date: 2016-02-02
Author: Kieran O'Neill, Mark Hills, Mike Gottlieb
Maintainer: Kieran O'Neill <koneill@bccrc.ca>
Description: Using strand inheritance data from multiple single cells
        from the organism whose genome is to be assembled, contiBAIT
        can cluster unbridged contigs together into putative
        chromosomes, and order the contigs within those chromosomes.
License: BSD_2_clause + file LICENSE
Depends: BH (>= 1.51.0-3), Rsamtools (>= 1.21)
LinkingTo: Rcpp, BH
Imports: grDevices, clue, cluster, gplots, IRanges, GenomicRanges,
        S4Vectors, Rcpp, TSP, GenomicFiles, gtools, rtracklayer,
        BiocParallel, DNAcopy, colorspace, reshape2, ggplot2, methods,
        exomeCopy, GenomicAlignments, diagram
Suggests: BiocStyle
biocViews: CellBasedAssays, QualityControl, WholeGenome, Genetics,
        GenomeAssembly
Collate: 'AllClasses.R' 'AllGenerics.R' 'BAIT.R'
        'barplotLinkageGroupCalls.R' 'clusterContigs.R'
        'computeConsensus.R' 'computeSim.R' 'contiBAIT.R'
        'findSimilarLibraries.R' 'fixLinkageGroups.R'
        'highlightAssemblyErrors.R' 'ideogramPlot.R'
        'locateMisorients.R' 'makeBoxPlot.R' 'makeChrTable.R'
        'mapGapFromOverlap.R' 'mergeFlankedLGs.R'
        'orderAllLinkageGroups.R' 'orderContigsGreedy.R'
        'orderContigsTSP.R' 'plotContigOrder.R' 'plotLGDistances.R'
        'plotWCdistribution.R' 'preprocessStrandTable.R'
        'reorientAndMergeLGs.R' 'strandSeqFreqTable.R' 'thoroughBed.R'
        'writeBed.R'
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2017-04-25 01:19:36 UTC; biocbuild
Built: R 3.4.0; i386-w64-mingw32; 2017-04-25 03:12:45 UTC; windows
Archs: i386, x64
