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