CNE detection and visualization.

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Documentation for package ‘CNEr’ version 1.2.0

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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"'