Man pages for CNEr
CNE Detection and Visualization

addAncestorGO	Add ancestor GO IDs
AssemblyStats	Assembly statistics.
axisTrack	Example data for plotting annotation.
axtChain	axtChain
Axt-class	Class '"Axt"'
axtInfo	axtInfo function
Axt-util	Utility functions related to Axt alignment
binner	UCSC bin indexing system utility functions
blatCNE	Wrapper function of blat for 'CNE' object
ceScan-methods	ceScan function
chainMergeSort	chainMergeSort
chainNetSyntenic	chainNetSyntenic
chainPreNet	chainPreNet
CNE-class	Class '"CNE"'
CNEDanRer10Hg38	CNEHg38DanRer10 and CNEDanRer10Hg38 dataset
CNEDensity	CNEDensity function
cneFinalListDanRer10Hg38	cneFinalListDanRer10Hg38 dataset
cneMerge	CNE merge function
fetchChromSizes	fetchChromSizes function.
fixCoordinates	Fix the coordinates in 'Axt' object
GRangePairs-class	GRangePairs objects
grangesPairsForDotplot	grangesPairsForDotplot
last	lastal wrapper
lastz	lastz wrapper
lavToPsl	lavToPsl
makeAncoraFiles	makeAncoraFiles
makeAxtTracks	makeAxtTracks
makeCNEDensity	Make 'Bed', 'bedGraph' and 'BigWig' files
makeGRBs	makeGRBs
matchDistribution	Plot the distribution of matched alignments.
netToAxt	netToAxt
orgKEGGIds2EntrezIDs	Fetch mapping from KEGG IDs to Entrez IDs
plotCNEDistribution	Plot sequential CNE number against CNE genomic location
plotCNEWidth	Plot the CNE widths distribution
psubAxt	Parallel subset of Axt alignment
queryCNEData	Query the CNEData package to fetch the CNEs
readAncora	Read the cne file from Ancora format.
readAncoraIntoSQLite	Read Ancora legacy CNE format
readAxt	Read 'Axt' file
readBed	Read bed file
readCNERangesFromSQLite	readCNERangesFromSQLite function
read.rmMask.GRanges	Read a RepeatMasker .out file
read.rmskFasta	Read a soft repeat masked fasta
reverseCigar	reverseCigar function
saveCNEToSQLite	Save CNE to SQLite
scoringMatrix	scoringMatrix
subAxt-methods	Subset an 'Axt' object
syntenicDotplot	Syntenic dotplot
writeAxt	'writeAxt' function