Man pages for CNEr
CNE Detection and Visualization

addAncestorGOAdd ancestor GO IDs
AssemblyStatsAssembly statistics.
axisTrackExample data for plotting annotation.
axtChainaxtChain
Axt-classClass '"Axt"'
axtInfoaxtInfo function
Axt-utilUtility functions related to Axt alignment
binnerUCSC bin indexing system utility functions
blatCNEWrapper function of blat for 'CNE' object
ceScan-methodsceScan function
chainMergeSortchainMergeSort
chainNetSyntenicchainNetSyntenic
chainPreNetchainPreNet
CNE-classClass '"CNE"'
CNEDanRer10Hg38CNEHg38DanRer10 and CNEDanRer10Hg38 dataset
CNEDensityCNEDensity function
cneFinalListDanRer10Hg38cneFinalListDanRer10Hg38 dataset
cneMergeCNE merge function
fetchChromSizesfetchChromSizes function.
fixCoordinatesFix the coordinates in 'Axt' object
GRangePairs-classGRangePairs objects
grangesPairsForDotplotgrangesPairsForDotplot
lastlastal wrapper
lastzlastz wrapper
lavToPsllavToPsl
makeAncoraFilesmakeAncoraFiles
makeAxtTracksmakeAxtTracks
makeCNEDensityMake 'Bed', 'bedGraph' and 'BigWig' files
makeGRBsmakeGRBs
matchDistributionPlot the distribution of matched alignments.
netToAxtnetToAxt
orgKEGGIds2EntrezIDsFetch mapping from KEGG IDs to Entrez IDs
plotCNEDistributionPlot sequential CNE number against CNE genomic location
plotCNEWidthPlot the CNE widths distribution
psubAxtParallel subset of Axt alignment
queryCNEDataQuery the CNEData package to fetch the CNEs
readAncoraRead the cne file from Ancora format.
readAncoraIntoSQLiteRead Ancora legacy CNE format
readAxtRead 'Axt' file
readBedRead bed file
readCNERangesFromSQLitereadCNERangesFromSQLite function
read.rmMask.GRangesRead a RepeatMasker .out file
read.rmskFastaRead a soft repeat masked fasta
reverseCigarreverseCigar function
saveCNEToSQLiteSave CNE to SQLite
scoringMatrixscoringMatrix
subAxt-methodsSubset an 'Axt' object
syntenicDotplotSyntenic dotplot
writeAxt'writeAxt' function
CNEr documentation built on Nov. 17, 2017, 9:54 a.m.