Package: contiBAIT
Type: Package
Title: Improves Early Build Genome Assemblies using Strand-Seq Data
Version: 1.30.0
Date: 2021-11-20
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: R (>= 3.5.0), BH (>= 1.51.0.3), Rsamtools (>= 1.21)
LinkingTo: Rcpp, BH
Imports: data.table, grDevices, clue, cluster, gplots, BiocGenerics (>=
        0.31.6), S4Vectors, IRanges, GenomicRanges, Rcpp, TSP,
        GenomicFiles, gtools, rtracklayer, BiocParallel, DNAcopy,
        colorspace, reshape2, ggplot2, methods, exomeCopy,
        GenomicAlignments, diagram
Suggests: BiocStyle
biocViews: ImmunoOncology, CellBasedAssays, QualityControl,
        WholeGenome, Genetics, GenomeAssembly
Collate: 'AllClasses.R' 'AllGenerics.R' 'BAIT.R'
        'barplotLinkageGroupCalls.R' 'clusterContigs.R'
        'computeConsensus.R' 'computeSim.R' 'contiBAIT.R'
        'findSexGroups.R' 'findSimilarLibraries.R' 'fixLinkageGroups.R'
        'flipOrderedLinkageGroups.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: 6.0.1.9000
NeedsCompilation: yes
git_url: https://git.bioconductor.org/packages/contiBAIT
git_branch: RELEASE_3_18
git_last_commit: 4d4e432
git_last_commit_date: 2023-10-24
Date/Publication: 2023-10-24
Packaged: 2023-10-24 20:49:09 UTC; biocbuild
Built: R 4.3.3; x86_64-apple-darwin13.4.0; 2024-05-29 21:32:34 UTC; unix
