contiBAIT: Improves Early Build Genome Assemblies using Strand-Seq Data

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.

AuthorKieran O'Neill, Mark Hills, Mike Gottlieb
Date of publicationNone
MaintainerKieran O'Neill <koneill@bccrc.ca>
LicenseBSD_2_clause + file LICENSE
Version1.2.0

View on Bioconductor

Man pages

BAIT: BAIT - master function to process strand-seq libraries into...

barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method: Bar plot all linkage groups, with the true chromosomes of...

ChrTable: A class for storing chromosome/fragment lengths

clusterContigs-StrandStateMatrix-method: clusterContigs - agglomeratively clusters contigs into...

contiBAIT: contiBAIT - master function to process strand-seq libraries...

ContigOrdering: A class for storing contig ordering of a linkage group

exampleChrTable: Example of a ChromosomeTable, containing contigs and their...

exampleContigOrder: Example of a ContigOrdering table, containing a list with a...

exampleCrickFreq: An example Crick strand frequences extracted from BAMS by...

exampleDividedChr: Example of a divided chromosome, containing contigs and their...

exampleLGList: Example of a LinkageGroupList output from clusterContigs

exampleLibList: Example of a LibraryGroupList, containing library names

exampleReadCounts: Example of read counts extracted from BAMS by...

exampleStrandFreq: Example of strand frequencies extracted from BAMS by...

exampleWatsonFreq: An example Watson strand frequences extracted from BAMS by...

exampleWCMatrix: An example StrandStateMatrix containing WW, CC and WC calls...

findSimilarLibraries: findSimilarLibraries - function to identify libraries that...

fixLinkageGroups: fixLinkageGroups - searches for discrepancies within ordered...

highlightAssemblyErrors: highlightAssemblyErrors - Master function to identify...

ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method: ideogramPlot - plots BAIT-like ideograms

LibraryGroupList: A class for storing library group calls for contigs

LinkageGroupList: A class for storing linkage group calls for contigs

locateMisorients: locateMisorients - function to identify libraries that hare...

makeBoxPlot: makeBoxPlot - creates boxplot of contigs included in the...

makeChrTable: makeChrTable - Pulls out chromosome and length data from the...

mapGapFromOverlap: mapGapFromOverlap - function to co-localize strand state...

mergeFlankedLGs: mergeFlankedLGs - searches for similarities at the ends of...

orderAllLinkageGroups: Function to call contig ordering algorithms iteratively...

orderContigsGreedy: Function to order contigs within a single linkage group using...

orderContigsTSP: Attempt to order contigs within linkage groups using...

OrientationFrame: A class for storing contig orientations

plotContigOrder: Plot ordering of contigs within a single linkage group.

plotLGDistances-LinkageGroupList-StrandStateMatrix-method: plotLGDistances - plots a heatmap of the distances between...

plotWCdistribution-StrandFreqMatrix-method: Creates median distribution boxplots across all libraries and...

preprocessStrandTable-StrandFreqMatrix-method: preprocessStrandTable - remove low quality libraries and...

reorientAndMergeLGs: reorientAndMergeLGs uses a simple dissimilarity to find...

show-ContigOrdering-method: show-methods

show-LibraryGroupList-method: show-methods

show-LinkageGroupList-method: show-methods

show-OrientationFrame-method: show-methods

show-StrandFreqMatrix-method: show-methods

show-StrandReadMatrix-method: show-methods

show-StrandStateList-method: show-methods

show-StrandStateMatrix-method: show-methods

StrandFreqMatrix: A class for storing a matrix of frequencies of Watson to...

StrandReadMatrix: A class for storing read counts for a set of contigs over...

strandSeqFreqTable: strandSeqFreqTable - function to process bam files for...

StrandStateList: A class for storing StrandStateList lists for contigs

StrandStateMatrix: A class for storing a data frame of discrete strand states of...

thoroughBed: thoroughBed - function to merge chromosomes from libraries...

writeBed: function to write contig order to BED file

Files in this package

contiBAIT/DESCRIPTION
contiBAIT/LICENSE
contiBAIT/NAMESPACE
contiBAIT/R
contiBAIT/R/AllClasses.R contiBAIT/R/AllGenerics.R contiBAIT/R/BAIT.R contiBAIT/R/barplotLinkageGroupCalls.R contiBAIT/R/clusterContigs.R contiBAIT/R/computeConsensus.R contiBAIT/R/computeSim.R contiBAIT/R/contiBAIT.R contiBAIT/R/findSimilarLibraries.R contiBAIT/R/fixLinkageGroups.R contiBAIT/R/highlightAssemblyErrors.R contiBAIT/R/ideogramPlot.R contiBAIT/R/locateMisorients.R contiBAIT/R/makeBoxPlot.R contiBAIT/R/makeChrTable.R contiBAIT/R/mapGapFromOverlap.R contiBAIT/R/mergeFlankedLGs.R contiBAIT/R/orderAllLinkageGroups.R contiBAIT/R/orderContigsGreedy.R contiBAIT/R/orderContigsTSP.R contiBAIT/R/plotContigOrder.R contiBAIT/R/plotLGDistances.R contiBAIT/R/plotWCdistribution.R contiBAIT/R/preprocessStrandTable.R contiBAIT/R/reorientAndMergeLGs.R contiBAIT/R/strandSeqFreqTable.R contiBAIT/R/thoroughBed.R contiBAIT/R/writeBed.R
contiBAIT/README.md
contiBAIT/build
contiBAIT/build/vignette.rds
contiBAIT/data
contiBAIT/data/exampleChrTable.rda
contiBAIT/data/exampleContigOrder.rda
contiBAIT/data/exampleCrickFreq.rda
contiBAIT/data/exampleDividedChr.rda
contiBAIT/data/exampleLGList.rda
contiBAIT/data/exampleLibList.rda
contiBAIT/data/exampleReadCounts.rda
contiBAIT/data/exampleStrandFreq.rda
contiBAIT/data/exampleWCMatrix.rda
contiBAIT/data/exampleWatsonFreq.rda
contiBAIT/inst
contiBAIT/inst/NEWS
contiBAIT/inst/doc
contiBAIT/inst/doc/contiBAIT.R
contiBAIT/inst/doc/contiBAIT.Rnw
contiBAIT/inst/doc/contiBAIT.pdf
contiBAIT/inst/examples
contiBAIT/inst/examples/BAIT.R
contiBAIT/inst/examples/barplotLinkageGroupCalls.R
contiBAIT/inst/examples/clusterContigs.R
contiBAIT/inst/examples/contiBAIT.R
contiBAIT/inst/examples/findSimilarLibraries.R
contiBAIT/inst/examples/ideogramPlot.R
contiBAIT/inst/examples/makeBoxPlot.R
contiBAIT/inst/examples/makeChrTable.R
contiBAIT/inst/examples/mapGapFromOverlap.R
contiBAIT/inst/examples/orderAllLinkageGroups.R
contiBAIT/inst/examples/plotContigOrder.R
contiBAIT/inst/examples/plotLGDistances.R
contiBAIT/inst/examples/plotWCdistribution.R
contiBAIT/inst/examples/preprocessStrandTable.R
contiBAIT/inst/examples/reorientAndMergeLGs.R
contiBAIT/inst/examples/strandSeqFreqTable.R
contiBAIT/inst/examples/thoroughBed.R
contiBAIT/inst/examples/writeBed.R
contiBAIT/inst/extdata
contiBAIT/inst/extdata/StrandSeqTestData_1.bam
contiBAIT/inst/extdata/StrandSeqTestData_10.bam
contiBAIT/inst/extdata/StrandSeqTestData_11.bam
contiBAIT/inst/extdata/StrandSeqTestData_12.bam
contiBAIT/inst/extdata/StrandSeqTestData_13.bam
contiBAIT/inst/extdata/StrandSeqTestData_14.bam
contiBAIT/inst/extdata/StrandSeqTestData_15.bam
contiBAIT/inst/extdata/StrandSeqTestData_16.bam
contiBAIT/inst/extdata/StrandSeqTestData_17.bam
contiBAIT/inst/extdata/StrandSeqTestData_18.bam
contiBAIT/inst/extdata/StrandSeqTestData_19.bam
contiBAIT/inst/extdata/StrandSeqTestData_2.bam
contiBAIT/inst/extdata/StrandSeqTestData_20.bam
contiBAIT/inst/extdata/StrandSeqTestData_21.bam
contiBAIT/inst/extdata/StrandSeqTestData_22.bam
contiBAIT/inst/extdata/StrandSeqTestData_23.bam
contiBAIT/inst/extdata/StrandSeqTestData_24.bam
contiBAIT/inst/extdata/StrandSeqTestData_25.bam
contiBAIT/inst/extdata/StrandSeqTestData_26.bam
contiBAIT/inst/extdata/StrandSeqTestData_27.bam
contiBAIT/inst/extdata/StrandSeqTestData_28.bam
contiBAIT/inst/extdata/StrandSeqTestData_29.bam
contiBAIT/inst/extdata/StrandSeqTestData_3.bam
contiBAIT/inst/extdata/StrandSeqTestData_30.bam
contiBAIT/inst/extdata/StrandSeqTestData_31.bam
contiBAIT/inst/extdata/StrandSeqTestData_32.bam
contiBAIT/inst/extdata/StrandSeqTestData_33.bam
contiBAIT/inst/extdata/StrandSeqTestData_34.bam
contiBAIT/inst/extdata/StrandSeqTestData_35.bam
contiBAIT/inst/extdata/StrandSeqTestData_4.bam
contiBAIT/inst/extdata/StrandSeqTestData_5.bam
contiBAIT/inst/extdata/StrandSeqTestData_6.bam
contiBAIT/inst/extdata/StrandSeqTestData_7.bam
contiBAIT/inst/extdata/StrandSeqTestData_8.bam
contiBAIT/inst/extdata/StrandSeqTestData_9.bam
contiBAIT/man
contiBAIT/man/BAIT.Rd contiBAIT/man/ChrTable.Rd contiBAIT/man/ContigOrdering.Rd contiBAIT/man/LibraryGroupList.Rd contiBAIT/man/LinkageGroupList.Rd contiBAIT/man/OrientationFrame.Rd contiBAIT/man/StrandFreqMatrix.Rd contiBAIT/man/StrandReadMatrix.Rd contiBAIT/man/StrandStateList.Rd contiBAIT/man/StrandStateMatrix.Rd contiBAIT/man/barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method.Rd contiBAIT/man/clusterContigs-StrandStateMatrix-method.Rd contiBAIT/man/contiBAIT.Rd contiBAIT/man/exampleChrTable.Rd contiBAIT/man/exampleContigOrder.Rd contiBAIT/man/exampleCrickFreq.Rd contiBAIT/man/exampleDividedChr.Rd contiBAIT/man/exampleLGList.Rd contiBAIT/man/exampleLibList.Rd contiBAIT/man/exampleReadCounts.Rd contiBAIT/man/exampleStrandFreq.Rd contiBAIT/man/exampleWCMatrix.Rd contiBAIT/man/exampleWatsonFreq.Rd contiBAIT/man/findSimilarLibraries.Rd contiBAIT/man/fixLinkageGroups.Rd contiBAIT/man/highlightAssemblyErrors.Rd contiBAIT/man/ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method.Rd contiBAIT/man/locateMisorients.Rd contiBAIT/man/makeBoxPlot.Rd contiBAIT/man/makeChrTable.Rd contiBAIT/man/mapGapFromOverlap.Rd contiBAIT/man/mergeFlankedLGs.Rd contiBAIT/man/orderAllLinkageGroups.Rd contiBAIT/man/orderContigsGreedy.Rd contiBAIT/man/orderContigsTSP.Rd contiBAIT/man/plotContigOrder.Rd contiBAIT/man/plotLGDistances-LinkageGroupList-StrandStateMatrix-method.Rd contiBAIT/man/plotWCdistribution-StrandFreqMatrix-method.Rd contiBAIT/man/preprocessStrandTable-StrandFreqMatrix-method.Rd contiBAIT/man/reorientAndMergeLGs.Rd contiBAIT/man/show-ContigOrdering-method.Rd contiBAIT/man/show-LibraryGroupList-method.Rd contiBAIT/man/show-LinkageGroupList-method.Rd contiBAIT/man/show-OrientationFrame-method.Rd contiBAIT/man/show-StrandFreqMatrix-method.Rd contiBAIT/man/show-StrandReadMatrix-method.Rd contiBAIT/man/show-StrandStateList-method.Rd contiBAIT/man/show-StrandStateMatrix-method.Rd contiBAIT/man/strandSeqFreqTable.Rd contiBAIT/man/thoroughBed.Rd contiBAIT/man/writeBed.Rd
contiBAIT/src
contiBAIT/src/Makevars
contiBAIT/src/Makevars.win
contiBAIT/src/computeSim.cpp
contiBAIT/src/computeSim.h
contiBAIT/src/orderContigsGreedy.cpp
contiBAIT/src/orderContigsGreedy.h
contiBAIT/vignettes
contiBAIT/vignettes/contiBAIT.Rnw

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