Files in Bioconductor-mirror/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/findSimilarLibraries.R R/fixLinkageGroups.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/OrientationFrame.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/findSimilarLibraries.Rd man/fixLinkageGroups.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/computeSim.cpp
src/computeSim.h
src/computeSim.o
src/contiBAIT.so
src/orderContigsGreedy.cpp
src/orderContigsGreedy.h
vignettes/contiBAIT.Rnw
vignettes/contiBAIT.tex
Bioconductor-mirror/contiBAIT documentation built on June 1, 2017, 6:40 a.m.