Files in CNEr

CNE Detection and Visualization

README.md

NEWS

NAMESPACE

DESCRIPTION

LICENSE

build/vignette.rds

src/R_init_CNEr.c

src/ceScan.c

src/Makevars.common

src/Makevars.win

src/utils.c

src/Makevars

src/S4Vectors_stubs.c

src/IRanges_stubs.c

src/XVector_stubs.c

src/io.c

src/CNEr.h

src/ucsc/mime.h

src/ucsc/chain.c

src/ucsc/kxTok.c

src/ucsc/net.h

src/ucsc/https.c

src/ucsc/sqlList.h

src/ucsc/pipeline.c

src/ucsc/common.h

src/ucsc/cirTree.h

src/ucsc/cirTree.c

src/ucsc/net.c

src/ucsc/_portimpl.c

src/ucsc/cheapcgi.c

src/ucsc/wildcmp.c

src/ucsc/servCrunx.c

src/ucsc/servcl.c

src/ucsc/axt.c

src/ucsc/_cheapcgi.c

src/ucsc/binRange.c

src/ucsc/_portimpl.h

src/ucsc/bits.h

src/ucsc/https.h

src/ucsc/dlist.h

src/ucsc/options.c

src/ucsc/udc.c

src/ucsc/localmem.c

src/ucsc/memalloc.c

src/ucsc/portable.h

src/ucsc/kxTok.h

src/ucsc/mime.c

src/ucsc/bits.c

src/ucsc/options.h

src/ucsc/localmem.h

src/ucsc/htmshell.h

src/ucsc/hash.c

src/ucsc/pipeline.h

src/ucsc/obscure.c

src/ucsc/base64.c

src/ucsc/cheapcgi.h

src/ucsc/axt.h

src/ucsc/dnaseq.h

src/ucsc/dnaseq.c

src/ucsc/dlist.c

src/ucsc/binRange.h

src/ucsc/errabort.h

src/ucsc/dystring.c

src/ucsc/memalloc.h

src/ucsc/common.c

src/ucsc/base64.h

src/ucsc/dnautil.c

src/ucsc/hash.h

src/ucsc/sqlList.c

src/ucsc/servpws.c

src/ucsc/errabort.c

src/ucsc/verbose.c

src/ucsc/servcis.c

src/ucsc/oswin9x.c

src/ucsc/intExp.c

src/ucsc/dnautil.h

src/ucsc/verbose.h

src/ucsc/linefile.h

src/ucsc/dystring.h

src/ucsc/servBrcMcw.c

src/ucsc/osunix.c

src/ucsc/os.c

src/ucsc/obscure.h

src/ucsc/sig.h

src/ucsc/chain.h

src/ucsc/sqlNum.h

src/ucsc/portimpl.c

src/ucsc/portimpl.h

src/ucsc/linefile.c

src/ucsc/servmsII.c

src/ucsc/sqlNum.c

src/ucsc/internet.c

src/ucsc/udc.h

src/ucsc/internet.h

data/grangesPairsForDotplot.rda

data/CNEDanRer10Hg38.rda

data/refGenes.rda

data/axisTrack.rda

data/CNEHg38DanRer10.rda

data/cpgIslands.rda

data/cneFinalListDanRer10Hg38.rda

R/GRB.R R/GRangePairs-class.R R/GO.R R/AssemblyStats.R R/makeGeneDbFromUCSC.R R/Ancora.R R/utils.R R/DB.R R/ceScan.R R/scoringMatrix.R R/CNE-class.R R/CNE-methods.R R/Axt-class.R R/WholeGenomeAlignment.R R/plot.R R/Axt-methods.R R/subAxt-methods.R R/IO-methods.R R/KEGG.R R/GRangePairs-methods.R vignettes/CNEr.Rmd vignettes/PairwiseWholeGenomeAlignment.Rmd

vignettes/CNEr.bib

man/syntenicDotplot.Rd man/orgKEGGIds2EntrezIDs.Rd man/Axt-util.Rd man/chainPreNet.Rd man/binner.Rd man/queryCNEData.Rd man/cneMerge.Rd man/cneFinalListDanRer10Hg38.Rd man/makeAncoraFiles.Rd man/ceScan-methods.Rd man/CNE-class.Rd man/lastz.Rd man/grangesPairsForDotplot.Rd man/readAncoraIntoSQLite.Rd man/netToAxt.Rd man/lavToPsl.Rd man/read.rmskFasta.Rd man/axtInfo.Rd man/makeAxtTracks.Rd man/reverseCigar.Rd man/GRangePairs-class.Rd man/fixCoordinates.Rd man/last.Rd man/writeAxt.Rd man/axisTrack.Rd man/chainMergeSort.Rd man/matchDistribution.Rd man/fetchChromSizes.Rd man/makeGRBs.Rd man/readAncora.Rd man/readAxt.Rd man/CNEDensity.Rd man/blatCNE.Rd man/axtChain.Rd man/Axt-class.Rd man/readBed.Rd man/saveCNEToSQLite.Rd man/AssemblyStats.Rd man/read.rmMask.GRanges.Rd man/subAxt-methods.Rd man/addAncestorGO.Rd man/scoringMatrix.Rd man/CNEDanRer10Hg38.Rd man/psubAxt.Rd man/makeCNEDensity.Rd man/chainNetSyntenic.Rd man/plotCNEDistribution.Rd man/plotCNEWidth.Rd man/readCNERangesFromSQLite.Rd tests/testthat.R tests/testthat/test_IO.R tests/testthat/test_GRBs.R tests/testthat/test_GRangePairs.R tests/testthat/test_ceScan.R tests/testthat/test_Axt.R tests/testthat/test_CNE.R tests/testthat/test_reverseCigar.R

inst/CITATION

inst/doc/CNEr.Rmd inst/doc/PairwiseWholeGenomeAlignment.Rmd

inst/doc/PairwiseWholeGenomeAlignment.html

inst/doc/CNEr.R inst/doc/PairwiseWholeGenomeAlignment.R

inst/doc/CNEr.html

inst/obsolete/alignment.c

inst/obsolete/CNEr.Rnw

inst/obsolete/class.r inst/obsolete/ceScan.r inst/obsolete/ceScanR.r

inst/obsolete/src/ceScan.c

inst/obsolete/src/ceScanBranch1.c

inst/obsolete/src/compile

inst/obsolete/src/ceScanBranch2.c

inst/extdata/cne2wBf_cypCar1_danRer10_100_100

inst/extdata/hg38.danRer10.net.axt

inst/extdata/cne2wBf_AstMex102_danRer10_48_50

inst/extdata/danRer10.hg38.net.axt

inst/extdata/filter_regions.hg38.bed

inst/extdata/danRer10CNE.sqlite

inst/extdata/cne2wBf_cteIde1_danRer10_100_100

inst/extdata/cne2wBf_danRer10_hg38_45_50

inst/extdata/filter_regions.danRer10.bed

inst/extdata/chr4.hg19.galGal3.net.axt.gz

inst/extdata/rmsk.fa

inst/scripts/prepareData.R inst/scripts/danRer10Pipeline.R

CNEr documentation built on Nov. 8, 2020, 5:36 p.m.