CNEr
CNE Detection and Visualization

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35
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CNEr: CNE Detection and Visualization
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API

API for CNEr
CNE Detection and Visualization

Global functions
.CNEDensityInternal Source code
.axt.show_frame_line Source code
.singleBinRestrictionString Source code
.subAxtWhole Source code
.unlist_list_of_GRangePairs Source code
.validateBinRanges Source code
Axt Man page Source code
Axt-class Man page
CNE Man page Source code
CNE-class Man page
CNE12 Man page
CNE12,CNE-method Man page
CNE21 Man page
CNE21,CNE-method Man page
CNEDanRer10Hg38 Man page
CNEDensity Man page Source code
CNEDensity,ANY,character,character,missing,missing-method Man page
CNEDensity,ANY,missing,character,character,character-method Man page
CNEDensity-methods Man page
CNEFinal Man page
CNEFinal,CNE-method Man page
CNEHg38DanRer10 Man page
CNEMerged Man page
CNEMerged,CNE-method Man page
EScore Source code
GRangePairs Man page Source code
GRangePairs-class Man page
N50 Man page Source code
N90 Man page Source code
NXX Source code
[,Axt,ANY,ANY-method Man page
[[,GRangePairs,ANY,ANY-method Man page
addAncestorGO Man page Source code
axisTrack Man page
axtChain Man page Source code
axtInfo Man page Source code
axtMatchDistribution Source code
binFromCoordRange Man page Source code
binRangesFromCoordRange Man page Source code
binRestrictionString Man page Source code
blatCNE Man page Source code
c,Axt-method Man page
c,GRangePairs-method Man page
ceScan Man page
ceScan,Axt-method Man page
ceScan,CNE-method Man page
ceScanAxt Source code
ceScanR Source code
chainMergeSort Man page Source code
chainNetSyntenic Man page Source code
chainPreNet Man page Source code
chr2colour Source code
class:GRangePairs Man page
cneFinalListDanRer10Hg38 Man page
cneMerge Man page
cneMerge,CNE,missing-method Man page
cneMerge,GRangePairs,GRangePairs-method Man page
cneMergeGRangePairs Source code
coerce,GRangePairs,GRanges-method Man page
coerce,GRangePairs,GRangesList-method Man page
compDNAStringSet Source code
cpgIslands Man page
fetchChromSizes Man page Source code
findGORoot Source code
first,GRangePairs-method Man page
fixCoordinates Man page
fixCoordinates,Axt-method Man page
getChildTerms Source code
grangesPairsForDotplot Man page
grglist,GRangePairs-method Man page
hierarchicGOTable Source code
last Man page
last,GRangePairs-method Man page
lastal Man page Source code
lastz Man page Source code
lavToPsl Man page Source code
length,Axt-method Man page
makeAncoraFiles Man page Source code
makeAxtTracks Man page Source code
makeCNEDensity Man page Source code
makeGRBs Man page Source code
makeReversedFilter Source code
matchDistribution Man page
matchDistribution,Axt-method Man page
my.system Source code
netToAxt Man page Source code
normargPriorParams Source code
normarg_scoringMat Source code
orgKEGGIds2EntrezIDs Man page Source code
plotCNEDistribution Man page Source code
plotCNEWidth Man page Source code
psubAxt Man page Source code
queryAnnotationSQLite Source code
queryCNEData Man page Source code
queryRanges Man page
queryRanges,Axt-method Man page
querySeqs Man page
querySeqs,Axt-method Man page
read.rmMask.GRanges Man page Source code
read.rmskFasta Man page Source code
readAncora Man page Source code
readAncoraIntoSQLite Man page Source code
readAxt Man page Source code
readBed Man page Source code
readCNERangesFromSQLite Man page Source code
readGAF Source code
refGenes Man page
reverseCigar Man page Source code
saveCNEToSQLite Man page Source code
score,Axt-method Man page
scoringMatrix Man page Source code
second,GRangePairs-method Man page
seqToAlignment Source code
seqinfo,GRangePairs-method Man page
seqinfoFn Source code
seqlengthsNA Source code
seqnames,GRangePairs-method Man page
show,GRangePairs-method Man page
showAxt Source code
strand,GRangePairs-method Man page
subAxt Man page
subAxt,Axt,GRanges,missing,missing-method Man page
subAxt,Axt,character,integer,integer-method Man page
subAxt,Axt,character,missing,missing-method Man page
subAxt,Axt,character,numeric,numeric-method Man page
subAxt-methods Man page
summary Man page
summary,Axt-method Man page
supportedUCSCtables Source code
swap Man page
swap,GRangePairs-method Man page
symCount Man page
symCount,Axt-method Man page
syntenicDotplot Man page
syntenicDotplot,Axt-method Man page
syntenicDotplot,GRangePairs-method Man page
syntenicPlotGRangePairs Source code
targetRanges Man page
targetRanges,Axt-method Man page
targetSeqs Man page
targetSeqs,Axt-method Man page
thresholds Man page
thresholds,CNE-method Man page
toSeqSnippet Source code
unique,GRangePairs-method Man page
unlist,GRangePairs-method Man page
validateLastz Source code
writeAxt Man page Source code
CNEr documentation built on Nov. 8, 2020, 5:36 p.m.

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