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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

Version

1.8.3

License

GPL-2 | file LICENSE

Issues

11

Pull Requests

0

Stars

3

Forks

5

Maintainer

Ge Tan

Last Published

February 15th, 2017

Functions in CNEr (1.8.3)

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