Man pages for Bioconductor-mirror/contiBAIT
Improves Early Build Genome Assemblies using Strand-Seq Data

BAITBAIT - master function to process strand-seq libraries into...
barplotLinkageGroupCalls-LinkageGroupList-ChrTable-methodBar plot all linkage groups, with the true chromosomes of...
ChrTableA class for storing chromosome/fragment lengths
clusterContigs-StrandStateMatrix-methodclusterContigs - agglomeratively clusters contigs into...
contiBAITcontiBAIT - master function to process strand-seq libraries...
ContigOrderingA class for storing contig ordering of a linkage group
exampleChrTableExample of a ChromosomeTable, containing contigs and their...
exampleContigOrderExample of a ContigOrdering table, containing a list with a...
exampleCrickFreqAn example Crick strand frequences extracted from BAMS by...
exampleDividedChrExample of a divided chromosome, containing contigs and their...
exampleLGListExample of a LinkageGroupList output from clusterContigs
exampleLibListExample of a LibraryGroupList, containing library names
exampleReadCountsExample of read counts extracted from BAMS by...
exampleStrandFreqExample of strand frequencies extracted from BAMS by...
exampleWatsonFreqAn example Watson strand frequences extracted from BAMS by...
exampleWCMatrixAn example StrandStateMatrix containing WW, CC and WC calls...
findSimilarLibrariesfindSimilarLibraries - function to identify libraries that...
fixLinkageGroupsfixLinkageGroups - searches for discrepancies within ordered...
highlightAssemblyErrorshighlightAssemblyErrors - Master function to identify...
ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-methodideogramPlot - plots BAIT-like ideograms
LibraryGroupListA class for storing library group calls for contigs
LinkageGroupListA class for storing linkage group calls for contigs
locateMisorientslocateMisorients - function to identify libraries that hare...
makeBoxPlotmakeBoxPlot - creates boxplot of contigs included in the...
makeChrTablemakeChrTable - Pulls out chromosome and length data from the...
mapGapFromOverlapmapGapFromOverlap - function to co-localize strand state...
mergeFlankedLGsmergeFlankedLGs - searches for similarities at the ends of...
orderAllLinkageGroupsFunction to call contig ordering algorithms iteratively...
orderContigsGreedyFunction to order contigs within a single linkage group using...
orderContigsTSPAttempt to order contigs within linkage groups using...
OrientationFrameA class for storing contig orientations
plotContigOrderPlot ordering of contigs within a single linkage group.
plotLGDistances-LinkageGroupList-StrandStateMatrix-methodplotLGDistances - plots a heatmap of the distances between...
plotWCdistribution-StrandFreqMatrix-methodCreates median distribution boxplots across all libraries and...
preprocessStrandTable-StrandFreqMatrix-methodpreprocessStrandTable - remove low quality libraries and...
reorientAndMergeLGsreorientAndMergeLGs uses a simple dissimilarity to find...
show-ContigOrdering-methodshow-methods
show-LibraryGroupList-methodshow-methods
show-LinkageGroupList-methodshow-methods
show-OrientationFrame-methodshow-methods
show-StrandFreqMatrix-methodshow-methods
show-StrandReadMatrix-methodshow-methods
show-StrandStateList-methodshow-methods
show-StrandStateMatrix-methodshow-methods
StrandFreqMatrixA class for storing a matrix of frequencies of Watson to...
StrandReadMatrixA class for storing read counts for a set of contigs over...
strandSeqFreqTablestrandSeqFreqTable - function to process bam files for...
StrandStateListA class for storing StrandStateList lists for contigs
StrandStateMatrixA class for storing a data frame of discrete strand states of...
thoroughBedthoroughBed - function to merge chromosomes from libraries...
writeBedfunction to write contig order to BED file
Bioconductor-mirror/contiBAIT documentation built on June 1, 2017, 6:40 a.m.