addAncestorGO           Add ancestor GO IDs
axisTrack               Example data for plotting annotation.
Axt-class               Class '"Axt"'
axtChain                axtChain
axtInfo                 axtInfo function
binFromCoordRange       UCSC bin indexing system utility functions
blatCNE                 Wrapper function of blat for 'CNE' object
ceScan                  ceScan function
chainMergeSort          chainMergeSort
chainNetSyntenic        chainNetSyntenic
chainPreNet             chainPreNet
CNE-class               Class '"CNE"'
CNEDanRer10Hg38         CNEHg38DanRer10 and CNEDanRer10Hg38 dataset
CNEDensity-methods      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
lastal                  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.
N50                     Assembly statistics.
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
read.rmMask.GRanges     Read a RepeatMasker .out file
read.rmskFasta          Read a soft repeat masked fasta
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
reverseCigar            reverseCigar function
saveCNEToSQLite         Save CNE to SQLite
scoringMatrix           scoringMatrix
subAxt-methods          Subset an 'Axt' object
summary                 Utility functions related to Axt alignment
syntenicDotplot         Syntenic dotplot
writeAxt                'writeAxt' function
