Files in contiBAIT

Improves Early Build Genome Assemblies using Strand-Seq Data

README.md

NAMESPACE

DESCRIPTION

LICENSE

build/vignette.rds

src/orderContigsGreedy.h

src/computeSim.h

src/Makevars.win

src/buildLinkageGroups.cpp

src/Makevars

src/orderContigsGreedy.cpp

src/computeSim.cpp

data/exampleReadCounts.rda

data/exampleWCMatrix.rda

data/exampleDividedChr.rda

data/exampleLGList.rda

data/exampleLibList.rda

data/exampleStrandFreq.rda

data/exampleWatsonFreq.rda

data/exampleContigOrder.rda

data/exampleCrickFreq.rda

data/exampleChrTable.rda

R/preprocessStrandTable.R R/barplotLinkageGroupCalls.R R/locateMisorients.R R/makeChrTable.R R/BAIT.R R/AllGenerics.R R/mergeFlankedLGs.R R/orderContigsGreedy.R R/highlightAssemblyErrors.R R/fixLinkageGroups.R R/flipOrderedLinkageGroups.R R/contiBAIT.R R/orderContigsTSP.R R/findSexGroups.R R/makeBoxPlot.R R/reorientAndMergeLGs.R R/clusterContigs.R R/thoroughBed.R R/mapGapFromOverlap.R R/AllClasses.R R/writeBed.R R/computeSim.R R/plotContigOrder.R R/orderAllLinkageGroups.R R/computeConsensus.R R/plotWCdistribution.R R/strandSeqFreqTable.R R/ideogramPlot.R R/findSimilarLibraries.R R/plotLGDistances.R

vignettes/contiBAIT.Rnw

man/exampleChrTable.Rd man/exampleContigOrder.Rd man/exampleStrandFreq.Rd man/makeChrTable.Rd man/show-LinkageGroupList-method.Rd man/StrandFreqMatrix.Rd man/makeBoxPlot.Rd man/fixLinkageGroups.Rd man/show-StrandReadMatrix-method.Rd man/plotLGDistances-LinkageGroupList-StrandStateMatrix-method.Rd man/show-StrandStateMatrix-method.Rd man/flipOrderedLinkageGroups.Rd man/clusterContigs-StrandStateMatrix-method.Rd man/exampleWatsonFreq.Rd man/exampleWCMatrix.Rd man/LibraryGroupList.Rd man/preprocessStrandTable-StrandFreqMatrix-method.Rd man/exampleDividedChr.Rd man/exampleLGList.Rd man/highlightAssemblyErrors.Rd man/StrandReadMatrix.Rd man/plotWCdistribution-StrandFreqMatrix-method.Rd man/exampleReadCounts.Rd man/findSimilarLibraries.Rd man/StrandStateList.Rd man/LinkageGroupList.Rd man/findSexGroups-LinkageGroupList-StrandStateMatrix-method.Rd man/locateMisorients.Rd man/orderContigsGreedy.Rd man/ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method.Rd man/orderAllLinkageGroups.Rd man/show-OrientationFrame-method.Rd man/ChrTable.Rd man/mergeFlankedLGs.Rd man/show-ContigOrdering-method.Rd man/contiBAIT.Rd man/thoroughBed.Rd man/exampleCrickFreq.Rd man/exampleLibList.Rd man/strandSeqFreqTable.Rd man/StrandStateMatrix.Rd man/reorientAndMergeLGs.Rd man/mapGapFromOverlap.Rd man/ContigOrdering.Rd man/show-StrandFreqMatrix-method.Rd man/writeBed.Rd man/plotContigOrder.Rd man/barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method.Rd man/orderContigsTSP.Rd man/show-StrandStateList-method.Rd man/BAIT.Rd man/show-LibraryGroupList-method.Rd

inst/NEWS

inst/doc/contiBAIT.R

inst/doc/contiBAIT.Rnw

inst/doc/contiBAIT.pdf

inst/extdata/StrandSeqTestData_26.bam

inst/extdata/StrandSeqTestData_1.bam

inst/extdata/StrandSeqTestData_10.bam

inst/extdata/StrandSeqTestData_15.bam

inst/extdata/StrandSeqTestData_5.bam

inst/extdata/StrandSeqTestData_2.bam

inst/extdata/StrandSeqTestData_12.bam

inst/extdata/StrandSeqTestData_20.bam

inst/extdata/StrandSeqTestData_14.bam

inst/extdata/StrandSeqTestData_22.bam

inst/extdata/StrandSeqTestData_31.bam

inst/extdata/StrandSeqTestData_7.bam

inst/extdata/StrandSeqTestData_3.bam

inst/extdata/StrandSeqTestData_17.bam

inst/extdata/StrandSeqTestData_23.bam

inst/extdata/StrandSeqTestData_18.bam

inst/extdata/StrandSeqTestData_34.bam

inst/extdata/StrandSeqTestData_28.bam

inst/extdata/StrandSeqTestData_27.bam

inst/extdata/StrandSeqTestData_21.bam

inst/extdata/StrandSeqTestData_30.bam

inst/extdata/StrandSeqTestData_32.bam

inst/extdata/StrandSeqTestData_4.bam

inst/extdata/StrandSeqTestData_35.bam

inst/extdata/StrandSeqTestData_6.bam

inst/extdata/StrandSeqTestData_16.bam

inst/extdata/StrandSeqTestData_29.bam

inst/extdata/StrandSeqTestData_19.bam

inst/extdata/StrandSeqTestData_25.bam

inst/extdata/StrandSeqTestData_24.bam

inst/extdata/StrandSeqTestData_8.bam

inst/extdata/StrandSeqTestData_11.bam

inst/extdata/StrandSeqTestData_33.bam

inst/extdata/StrandSeqTestData_9.bam

inst/extdata/StrandSeqTestData_13.bam

inst/examples/preprocessStrandTable.R inst/examples/barplotLinkageGroupCalls.R inst/examples/makeChrTable.R inst/examples/BAIT.R inst/examples/contiBAIT.R inst/examples/makeBoxPlot.R inst/examples/reorientAndMergeLGs.R inst/examples/clusterContigs.R inst/examples/thoroughBed.R inst/examples/mapGapFromOverlap.R inst/examples/writeBed.R inst/examples/plotContigOrder.R inst/examples/orderAllLinkageGroups.R inst/examples/plotWCdistribution.R inst/examples/strandSeqFreqTable.R inst/examples/ideogramPlot.R inst/examples/findSimilarLibraries.R inst/examples/plotLGDistances.R

contiBAIT documentation built on Nov. 8, 2020, 5:49 p.m.