# CNE detection and visualization.

## Documentation for package ‘CNEr’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

assembly1 | Class '"CNE"'
assembly1-method | Class '"CNE"'
assembly2 | Class '"CNE"'
assembly2-method | Class '"CNE"'
axisTrack | Example data for plotting annotation.
Axt | Class '"Axt"'
Axt-class | Class '"Axt"'
axtDanRer7Hg19 | The dataset axtDanRer7Hg19, axtHg19DanRer7
axtHg19DanRer7 | The dataset axtDanRer7Hg19, axtHg19DanRer7
axtInfo | axtInfo function
binFromCoordRange | UCSC bin indexing system utility functions
binRangesFromCoordRange | UCSC bin indexing system utility functions
binRestrictionString | UCSC bin indexing system utility functions
blatCNE | Wrapper function of blat for CNEs
c-method | Class '"Axt"'
ceScan | ceScan function
ceScan-method | ceScan function
ceScan-methods | ceScan function
ceScanOneStep | ceScanOneStep function
CNE | Class '"CNE"'
CNE-class | Class '"CNE"'
CNE1 | Class '"CNE"'
CNE1-method | Class '"CNE"'
CNE2 | Class '"CNE"'
CNE2-method | Class '"CNE"'
cneBlatedDanRer7Hg19 | The dataset cneBlatedDanRer7Hg19
CNEDanRer7Hg19 | CNEHg19DanRer7 and CNEHg19DanRer7 dataset
CNEDensity | CNEDensity function
CNEDensity-method | CNEDensity function
CNEDensity-methods | CNEDensity function
CNEHg19DanRer7 | CNEHg19DanRer7 and CNEHg19DanRer7 dataset
cneHg19DanRer7_45_50 | These datasets of CNE density values.
cneHg19DanRer7_48_50 | These datasets of CNE density values.
cneHg19DanRer7_49_50 | These datasets of CNE density values.
cneMerge | CNE merge function
CNEMerged | Class '"CNE"'
CNEMerged-method | Class '"CNE"'
CNERepeatsFiltered | Class '"CNE"'
CNERepeatsFiltered-method | Class '"CNE"'
cpgIslands | Example data for plotting annotation.
fetchChromSizes | fetchChromSizes function.
finalCNE | finalCNE dataset
ideoTrack | Example data for plotting annotation.
length-method | Class '"Axt"'
nchar-method | Class '"Axt"'
qSizesDanRer7 | The chromosome sizes data.
qSizesHg19 | The chromosome sizes data.
queryCNEData | Query the CNEData package to fetch the CNEs
queryRanges | Class '"Axt"'
queryRanges-method | Class '"Axt"'
querySeqs | Class '"Axt"'
querySeqs-method | Class '"Axt"'
readAxt | readAxt function.
readBed | readBed function
readCNERangesFromSQLite | readCNERangesFromSQLite function
refGenes | Example data for plotting annotation.
reverseCigar | reverseCigar function
saveCNEToSQLite | saveCNEToSQLite function
saveCNEToSQLite-method | saveCNEToSQLite function
saveCNEToSQLite-methods | saveCNEToSQLite function
score-method | Class '"Axt"'
subAxt | 'subAxt' method
subAxt-method | 'subAxt' method
subAxt-methods | 'subAxt' method
symCount | Class '"Axt"'
symCount-method | Class '"Axt"'
targetRanges | Class '"Axt"'
targetRanges-method | Class '"Axt"'
targetSeqs | Class '"Axt"'
targetSeqs-method | Class '"Axt"'
thresholds | Class '"CNE"'
thresholds-method | Class '"CNE"'
writeAxt | 'writeAxt' function
[-method | Class '"Axt"'