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CNEr (version 1.8.3)
CNE Detection and Visualization
Description
Large-scale identification and advanced visualization of sets of conserved noncoding elements.
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Version
1.8.3
License
GPL-2 | file LICENSE
Issues
10
Pull Requests
0
Stars
3
Forks
5
Repository
https://github.com/ge11232002/CNEr
Maintainer
Ge Tan
Last Published
April 12th, 2016
Functions in CNEr (1.8.3)
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Axt-class
Class
"Axt"
axtChain
axtChain
CNEDanRer7Hg19
CNEHg19DanRer7 and CNEHg19DanRer7 dataset
axtDanRer7Hg19
The dataset axtDanRer7Hg19, axtHg19DanRer7
readAxt
readAxt
cneMerge
CNE merge function
readBed
readBed
chainNetSyntenic
chainNetSyntenic
mismatchSummary
Utility functions related to Axt alignment
chainPreNet
chainPreNet
GRangePairs-class
GRangePairs objects
lastal
lastal wrapper
blatCNE
Wrapper function of blat for CNEs
ceScan-methods
ceScan function
ceScanOneStep
ceScanOneStep function
chainMergeSort
chainMergeSort
qSizesDanRer7
The chromosome sizes data.
writeAxt
writeAxt
function
subAxt-methods
subAxt
method
queryCNEData
Query the CNEData package to fetch the CNEs
CNEDensity-methods
CNEDensity function
cneHg19DanRer7_45_50
These datasets of CNE density values.
lastz
lastz wrapper
lavToPsl
lavToPsl
CNE-class
Class
"CNE"
cneBlatedDanRer7Hg19
The dataset cneBlatedDanRer7Hg19
N50
Assembly statistics.
axisTrack
Example data for plotting annotation.
makeGRBs
makeGRBs
readCNERangesFromSQLite
readCNERangesFromSQLite function
netToAxt
netToAxt
reverseCigar
reverseCigar function
axtInfo
axtInfo function
binning-utils
UCSC bin indexing system utility functions
fetchChromSizes
fetchChromSizes function.
finalCNE
finalCNE dataset
saveCNEToSQLite-methods
saveCNEToSQLite function
scoringMatrix
scoringMatrix