Files in CNEr
CNE Detection and Visualization

NAMESPACE
README.md
LICENSE
NEWS
DESCRIPTION
configure.ac
R/Ancora.R R/GO.R R/scoringMatrix.R R/subAxt-methods.R R/Axt-class.R R/IO-methods.R R/makeGeneDbFromUCSC.R R/KEGG.R R/CNE-class.R R/DB.R R/GRangePairs-methods.R R/AssemblyStats.R R/GRB.R R/Axt-methods.R R/CNE-methods.R R/utils.R R/WholeGenomeAlignment.R R/ceScan.R R/plot.R R/GRangePairs-class.R inst/obsolete/class.r inst/obsolete/ceScan.r
inst/obsolete/CNEr.Rnw
inst/obsolete/ceScanR.r
inst/obsolete/src/ceScanBranch2.c
inst/obsolete/src/ceScan.c
inst/obsolete/src/ceScanBranch1.c
inst/obsolete/src/compile
inst/doc/CNEr.R
inst/doc/CNEr.html
inst/doc/PairwiseWholeGenomeAlignment.html
inst/doc/PairwiseWholeGenomeAlignment.Rmd inst/doc/PairwiseWholeGenomeAlignment.R inst/doc/CNEr.Rmd inst/scripts/prepareData.R inst/scripts/danRer10Pipeline.R
inst/extdata/cne2wBf_cypCar1_danRer10_100_100
inst/extdata/chr4.hg19.galGal3.net.axt.gz
inst/extdata/hg38.danRer10.net.axt
inst/extdata/cne2wBf_AstMex102_danRer10_48_50
inst/extdata/filter_regions.danRer10.bed
inst/extdata/danRer10CNE.sqlite
inst/extdata/rmsk.fa
inst/extdata/danRer10.hg38.net.axt
inst/extdata/filter_regions.hg38.bed
inst/extdata/cne2wBf_cteIde1_danRer10_100_100
inst/extdata/cne2wBf_danRer10_hg38_45_50
build/vignette.rds
tests/testthat.R tests/testthat/test_GRangePairs.R tests/testthat/test_CNE.R tests/testthat/test_ceScan.R tests/testthat/test_GRBs.R tests/testthat/test_IO.R tests/testthat/test_reverseCigar.R tests/testthat/test_Axt.R man/writeAxt.Rd man/chainPreNet.Rd man/psubAxt.Rd man/chainMergeSort.Rd man/readAncora.Rd man/read.rmMask.GRanges.Rd man/makeGRBs.Rd man/binner.Rd man/chainNetSyntenic.Rd man/axtInfo.Rd man/readAncoraIntoSQLite.Rd man/ceScan-methods.Rd man/reverseCigar.Rd man/plotCNEWidth.Rd man/makeAxtTracks.Rd man/readAxt.Rd man/Axt-util.Rd man/CNE-class.Rd man/subAxt-methods.Rd man/GRangePairs-class.Rd man/makeAncoraFiles.Rd man/plotCNEDistribution.Rd man/axtChain.Rd man/fixCoordinates.Rd man/addAncestorGO.Rd man/CNEDanRer10Hg38.Rd man/AssemblyStats.Rd man/read.rmskFasta.Rd man/cneFinalListDanRer10Hg38.Rd man/last.Rd man/Axt-class.Rd man/saveCNEToSQLite.Rd man/netToAxt.Rd man/cneMerge.Rd man/fetchChromSizes.Rd man/queryCNEData.Rd man/matchDistribution.Rd man/scoringMatrix.Rd man/blatCNE.Rd man/readCNERangesFromSQLite.Rd man/makeCNEDensity.Rd man/grangesPairsForDotplot.Rd man/CNEDensity.Rd man/lavToPsl.Rd man/axisTrack.Rd man/readBed.Rd man/lastz.Rd man/orgKEGGIds2EntrezIDs.Rd man/syntenicDotplot.Rd vignettes/CNEr.Rmd
vignettes/CNEr.bib
vignettes/PairwiseWholeGenomeAlignment.Rmd
data/CNEHg38DanRer10.rda
data/cneFinalListDanRer10Hg38.rda
data/axisTrack.rda
data/grangesPairsForDotplot.rda
data/CNEDanRer10Hg38.rda
data/refGenes.rda
data/cpgIslands.rda
src/Makevars.win
src/Makevars
src/CNEr.h
src/R_init_CNEr.c
src/XVector_stubs.c
src/S4Vectors_stubs.c
src/utils.c
src/alignment.c
src/ceScan.c
src/Makevars.common
src/io.c
src/IRanges_stubs.c
src/ucsc/net.c
src/ucsc/servBrcMcw.c
src/ucsc/dnaseq.c
src/ucsc/wildcmp.c
src/ucsc/servpws.c
src/ucsc/localmem.h
src/ucsc/base64.c
src/ucsc/internet.c
src/ucsc/osunix.c
src/ucsc/errabort.c
src/ucsc/memalloc.h
src/ucsc/https.h
src/ucsc/bits.c
src/ucsc/axt.h
src/ucsc/portimpl.c
src/ucsc/dnautil.h
src/ucsc/cirTree.c
src/ucsc/oswin9x.c
src/ucsc/obscure.c
src/ucsc/hash.c
src/ucsc/binRange.h
src/ucsc/servmsII.c
src/ucsc/dlist.c
src/ucsc/sqlNum.c
src/ucsc/servCrunx.c
src/ucsc/_portimpl.c
src/ucsc/verbose.h
src/ucsc/dystring.c
src/ucsc/kxTok.c
src/ucsc/sqlList.c
src/ucsc/mime.c
src/ucsc/pipeline.c
src/ucsc/portable.h
src/ucsc/common.h
src/ucsc/udc.c
src/ucsc/cheapcgi.h
src/ucsc/linefile.c
src/ucsc/chain.h
src/ucsc/options.c
src/ucsc/obscure.h
src/ucsc/hash.h
src/ucsc/binRange.c
src/ucsc/dlist.h
src/ucsc/sqlNum.h
src/ucsc/servcl.c
src/ucsc/https.c
src/ucsc/bits.h
src/ucsc/axt.c
src/ucsc/portimpl.h
src/ucsc/dnautil.c
src/ucsc/cirTree.h
src/ucsc/localmem.c
src/ucsc/base64.h
src/ucsc/internet.h
src/ucsc/servcis.c
src/ucsc/errabort.h
src/ucsc/memalloc.c
src/ucsc/_cheapcgi.c
src/ucsc/net.h
src/ucsc/dnaseq.h
src/ucsc/cheapcgi.c
src/ucsc/linefile.h
src/ucsc/chain.c
src/ucsc/options.h
src/ucsc/htmshell.h
src/ucsc/common.c
src/ucsc/udc.h
src/ucsc/os.c
src/ucsc/mime.h
src/ucsc/pipeline.h
src/ucsc/intExp.c
src/ucsc/_portimpl.h
src/ucsc/verbose.c
src/ucsc/dystring.h
src/ucsc/sig.h
src/ucsc/kxTok.h
src/ucsc/sqlList.h
CNEr documentation built on Nov. 17, 2017, 9:54 a.m.