CNEr: CNE Detection and Visualization

Large-scale identification and advanced visualization of sets of conserved noncoding elements.

AuthorGe Tan <ge.tan09@imperial.ac.uk>
Date of publicationNone
MaintainerGe Tan <ge.tan09@imperial.ac.uk>
LicenseGPL-2 | file LICENSE
Version1.10.2
https://github.com/ge11232002/CNEr

View on Bioconductor

Man pages

AssemblyStats: Assembly statistics.

axisTrack: Example data for plotting annotation.

axtChain: axtChain

Axt-class: Class '"Axt"'

axtInfo: axtInfo function

Axt-util: Utility functions related to Axt alignment

binner: UCSC bin indexing system utility functions

blatCNE: Wrapper function of blat for 'CNE' object

ceScan-methods: ceScan function

chainMergeSort: chainMergeSort

chainNetSyntenic: chainNetSyntenic

chainPreNet: chainPreNet

CNE-class: Class '"CNE"'

CNEDanRer10Hg38: CNEHg38DanRer10 and CNEDanRer10Hg38 dataset

CNEDensity: CNEDensity function

cneFinalListDanRer10Hg38: cneFinalListDanRer10Hg38 dataset

cneMerge: CNE merge function

fetchChromSizes: fetchChromSizes function.

fixCoordinates: Fix the coordinates in 'Axt' object

GRangePairs-class: GRangePairs objects

grangesPairsForDotplot: grangesPairsForDotplot

last: lastal wrapper

lastz: lastz wrapper

lavToPsl: lavToPsl

makeAncoraFiles: makeAncoraFiles

makeCNEDensity: Make 'Bed', 'bedGraph' and 'BigWig' files

makeGRBs: makeGRBs

matchDistribution: Plot the distribution of matched alignments.

netToAxt: netToAxt

orgKEGGIds2EntrezIDs: Fetch mapping from KEGG IDs to Entrez IDs

plotCNEDistribution: Plot sequential CNE number against CNE genomic location

plotCNEWidth: Plot the CNE widths distribution

psubAxt: Parallel subset of Axt alignment

queryCNEData: Query the CNEData package to fetch the CNEs

readAncora: Read the cne file from Ancora format.

readAncoraIntoSQLite: Read Ancora legacy CNE format

readAxt: Read 'Axt' file

readBed: Read bed file

readCNERangesFromSQLite: readCNERangesFromSQLite function

read.rmMask.GRanges: Read a RepeatMasker .out file

read.rmskFasta: Read a soft repeat masked fasta

reverseCigar: reverseCigar function

saveCNEToSQLite: Save CNE to SQLite

scoringMatrix: scoringMatrix

subAxt-methods: Subset an 'Axt' object

syntenicDotplot: Syntenic dotplot

writeAxt: 'writeAxt' function

Functions

axisTrack Man page
Axt Man page
[,Axt,ANY,ANY-method Man page
axtChain Man page
Axt-class Man page
axtInfo Man page
binFromCoordRange Man page
binRangesFromCoordRange Man page
binRestrictionString Man page
blatCNE Man page
c,Axt-method Man page
ceScan Man page
ceScan,Axt-method Man page
ceScan,CNE-method Man page
c,GRangePairs-method Man page
chainMergeSort Man page
chainNetSyntenic Man page
chainPreNet Man page
class:GRangePairs Man page
CNE Man page
CNE12 Man page
CNE12,CNE-method Man page
CNE21 Man page
CNE21,CNE-method Man page
CNE-class Man page
CNEDanRer10Hg38 Man page
CNEDensity Man page
CNEDensity,ANY,character,character,missing,missing-method Man page
CNEDensity,ANY,missing,character,character,character-method Man page
CNEDensity-methods Man page
CNEFinal Man page
CNEFinal,CNE-method Man page
cneFinalListDanRer10Hg38 Man page
CNEHg38DanRer10 Man page
cneMerge Man page
cneMerge,CNE,missing-method Man page
CNEMerged Man page
CNEMerged,CNE-method Man page
cneMerge,GRangePairs,GRangePairs-method Man page
coerce,GRangePairs,GRangesList-method Man page
coerce,GRangePairs,GRanges-method Man page
cpgIslands Man page
fetchChromSizes Man page
first,GRangePairs-method Man page
fixCoordinates Man page
fixCoordinates,Axt-method Man page
GRangePairs Man page
[[,GRangePairs,ANY,ANY-method Man page
GRangePairs-class Man page
grangesPairsForDotplot Man page
grglist,GRangePairs-method Man page
last Man page
lastal Man page
last,GRangePairs-method Man page
lastz Man page
lavToPsl Man page
length,Axt-method Man page
makeAncoraFiles Man page
makeCNEDensity Man page
makeGRBs Man page
matchDistribution Man page
matchDistribution,Axt-method Man page
N50 Man page
N90 Man page
netToAxt Man page
orgKEGGIds2EntrezIDs Man page
plotCNEDistribution Man page
plotCNEWidth Man page
psubAxt Man page
queryCNEData Man page
queryRanges Man page
queryRanges,Axt-method Man page
querySeqs Man page
querySeqs,Axt-method Man page
readAncora Man page
readAncoraIntoSQLite Man page
readAxt Man page
readBed Man page
readCNERangesFromSQLite Man page
read.rmMask.GRanges Man page
read.rmskFasta Man page
refGenes Man page
reverseCigar Man page
saveCNEToSQLite Man page
score,Axt-method Man page
scoringMatrix Man page
second,GRangePairs-method Man page
seqinfo,GRangePairs-method Man page
seqnames,GRangePairs-method Man page
show,GRangePairs-method Man page
strand,GRangePairs-method Man page
subAxt Man page
subAxt,Axt,character,integer,integer-method Man page
subAxt,Axt,character,missing,missing-method Man page
subAxt,Axt,character,numeric,numeric-method Man page
subAxt,Axt,GRanges,missing,missing-method Man page
subAxt-methods Man page
summary Man page
summary,Axt-method Man page
swap Man page
swap,GRangePairs-method Man page
symCount Man page
symCount,Axt-method Man page
syntenicDotplot Man page
syntenicDotplot,Axt-method Man page
syntenicDotplot,GRangePairs-method Man page
targetRanges Man page
targetRanges,Axt-method Man page
targetSeqs Man page
targetSeqs,Axt-method Man page
thresholds Man page
thresholds,CNE-method Man page
unique,GRangePairs-method Man page
unlist,GRangePairs-method Man page
writeAxt Man page

Files

CNEr/DESCRIPTION
CNEr/LICENSE
CNEr/NAMESPACE
CNEr/NEWS
CNEr/R
CNEr/R/Ancora.R CNEr/R/AssemblyStats.R CNEr/R/Axt-class.R CNEr/R/Axt-methods.R CNEr/R/CNE-class.R CNEr/R/CNE-methods.R CNEr/R/DB.R CNEr/R/GO.R CNEr/R/GRB.R CNEr/R/GRangePairs-class.R CNEr/R/GRangePairs-methods.R CNEr/R/IO-methods.R CNEr/R/KEGG.R CNEr/R/WholeGenomeAlignment.R CNEr/R/ceScan.R CNEr/R/makeGeneDbFromUCSC.R CNEr/R/plot.R CNEr/R/scoringMatrix.R CNEr/R/subAxt-methods.R CNEr/R/utils.R
CNEr/build
CNEr/build/vignette.rds
CNEr/configure.ac
CNEr/data
CNEr/data/CNEDanRer10Hg38.rda
CNEr/data/CNEHg38DanRer10.rda
CNEr/data/axisTrack.rda
CNEr/data/cneFinalListDanRer10Hg38.rda
CNEr/data/cpgIslands.rda
CNEr/data/grangesPairsForDotplot.rda
CNEr/data/refGenes.rda
CNEr/inst
CNEr/inst/doc
CNEr/inst/doc/CNEr.R
CNEr/inst/doc/CNEr.Rmd
CNEr/inst/doc/CNEr.html
CNEr/inst/doc/PairwiseWholeGenomeAlignment.R
CNEr/inst/doc/PairwiseWholeGenomeAlignment.Rmd
CNEr/inst/doc/PairwiseWholeGenomeAlignment.html
CNEr/inst/extdata
CNEr/inst/extdata/chr4.hg19.galGal3.net.axt.gz
CNEr/inst/extdata/cne2wBf_AstMex102_danRer10_48_50
CNEr/inst/extdata/cne2wBf_cteIde1_danRer10_100_100
CNEr/inst/extdata/cne2wBf_cypCar1_danRer10_100_100
CNEr/inst/extdata/cne2wBf_danRer10_hg38_45_50
CNEr/inst/extdata/danRer10.hg38.net.axt
CNEr/inst/extdata/danRer10CNE.sqlite
CNEr/inst/extdata/filter_regions.danRer10.bed
CNEr/inst/extdata/filter_regions.hg38.bed
CNEr/inst/extdata/hg38.danRer10.net.axt
CNEr/inst/extdata/rmsk.fa
CNEr/inst/obsolete
CNEr/inst/obsolete/CNEr.Rnw
CNEr/inst/obsolete/ceScan.r
CNEr/inst/obsolete/ceScanR.r
CNEr/inst/obsolete/class.r
CNEr/inst/obsolete/src
CNEr/inst/obsolete/src/ceScan.c
CNEr/inst/obsolete/src/ceScanBranch1.c
CNEr/inst/obsolete/src/ceScanBranch2.c
CNEr/inst/obsolete/src/compile
CNEr/inst/scripts
CNEr/inst/scripts/danRer10Pipeline.R
CNEr/inst/scripts/prepareData.R
CNEr/man
CNEr/man/AssemblyStats.Rd CNEr/man/Axt-class.Rd CNEr/man/Axt-util.Rd CNEr/man/CNE-class.Rd CNEr/man/CNEDanRer10Hg38.Rd CNEr/man/CNEDensity.Rd CNEr/man/GRangePairs-class.Rd CNEr/man/axisTrack.Rd CNEr/man/axtChain.Rd CNEr/man/axtInfo.Rd CNEr/man/binner.Rd CNEr/man/blatCNE.Rd CNEr/man/ceScan-methods.Rd CNEr/man/chainMergeSort.Rd CNEr/man/chainNetSyntenic.Rd CNEr/man/chainPreNet.Rd CNEr/man/cneFinalListDanRer10Hg38.Rd CNEr/man/cneMerge.Rd CNEr/man/fetchChromSizes.Rd CNEr/man/fixCoordinates.Rd CNEr/man/grangesPairsForDotplot.Rd CNEr/man/last.Rd CNEr/man/lastz.Rd CNEr/man/lavToPsl.Rd CNEr/man/makeAncoraFiles.Rd CNEr/man/makeCNEDensity.Rd CNEr/man/makeGRBs.Rd CNEr/man/matchDistribution.Rd CNEr/man/netToAxt.Rd CNEr/man/orgKEGGIds2EntrezIDs.Rd CNEr/man/plotCNEDistribution.Rd CNEr/man/plotCNEWidth.Rd CNEr/man/psubAxt.Rd CNEr/man/queryCNEData.Rd CNEr/man/read.rmMask.GRanges.Rd CNEr/man/read.rmskFasta.Rd CNEr/man/readAncora.Rd CNEr/man/readAncoraIntoSQLite.Rd CNEr/man/readAxt.Rd CNEr/man/readBed.Rd CNEr/man/readCNERangesFromSQLite.Rd CNEr/man/reverseCigar.Rd CNEr/man/saveCNEToSQLite.Rd CNEr/man/scoringMatrix.Rd CNEr/man/subAxt-methods.Rd CNEr/man/syntenicDotplot.Rd CNEr/man/writeAxt.Rd
CNEr/src
CNEr/src/CNEr.h
CNEr/src/IRanges_stubs.c
CNEr/src/Makevars
CNEr/src/Makevars.common
CNEr/src/Makevars.win
CNEr/src/R_init_CNEr.c
CNEr/src/S4Vectors_stubs.c
CNEr/src/XVector_stubs.c
CNEr/src/alignment.c
CNEr/src/ceScan.c
CNEr/src/io.c
CNEr/src/ucsc
CNEr/src/ucsc/_cheapcgi.c
CNEr/src/ucsc/_portimpl.c
CNEr/src/ucsc/_portimpl.h
CNEr/src/ucsc/axt.c
CNEr/src/ucsc/axt.h
CNEr/src/ucsc/base64.c
CNEr/src/ucsc/base64.h
CNEr/src/ucsc/binRange.c
CNEr/src/ucsc/binRange.h
CNEr/src/ucsc/bits.c
CNEr/src/ucsc/bits.h
CNEr/src/ucsc/chain.c
CNEr/src/ucsc/chain.h
CNEr/src/ucsc/cheapcgi.c
CNEr/src/ucsc/cheapcgi.h
CNEr/src/ucsc/cirTree.c
CNEr/src/ucsc/cirTree.h
CNEr/src/ucsc/common.c
CNEr/src/ucsc/common.h
CNEr/src/ucsc/dlist.c
CNEr/src/ucsc/dlist.h
CNEr/src/ucsc/dnaseq.c
CNEr/src/ucsc/dnaseq.h
CNEr/src/ucsc/dnautil.c
CNEr/src/ucsc/dnautil.h
CNEr/src/ucsc/dystring.c
CNEr/src/ucsc/dystring.h
CNEr/src/ucsc/errabort.c
CNEr/src/ucsc/errabort.h
CNEr/src/ucsc/hash.c
CNEr/src/ucsc/hash.h
CNEr/src/ucsc/htmshell.h
CNEr/src/ucsc/https.c
CNEr/src/ucsc/https.h
CNEr/src/ucsc/intExp.c
CNEr/src/ucsc/internet.c
CNEr/src/ucsc/internet.h
CNEr/src/ucsc/kxTok.c
CNEr/src/ucsc/kxTok.h
CNEr/src/ucsc/linefile.c
CNEr/src/ucsc/linefile.h
CNEr/src/ucsc/localmem.c
CNEr/src/ucsc/localmem.h
CNEr/src/ucsc/memalloc.c
CNEr/src/ucsc/memalloc.h
CNEr/src/ucsc/mime.c
CNEr/src/ucsc/mime.h
CNEr/src/ucsc/net.c
CNEr/src/ucsc/net.h
CNEr/src/ucsc/obscure.c
CNEr/src/ucsc/obscure.h
CNEr/src/ucsc/options.c
CNEr/src/ucsc/options.h
CNEr/src/ucsc/os.c
CNEr/src/ucsc/osunix.c
CNEr/src/ucsc/oswin9x.c
CNEr/src/ucsc/pipeline.c
CNEr/src/ucsc/pipeline.h
CNEr/src/ucsc/portable.h
CNEr/src/ucsc/portimpl.c
CNEr/src/ucsc/portimpl.h
CNEr/src/ucsc/servBrcMcw.c
CNEr/src/ucsc/servCrunx.c
CNEr/src/ucsc/servcis.c
CNEr/src/ucsc/servcl.c
CNEr/src/ucsc/servmsII.c
CNEr/src/ucsc/servpws.c
CNEr/src/ucsc/sig.h
CNEr/src/ucsc/sqlList.c
CNEr/src/ucsc/sqlList.h
CNEr/src/ucsc/sqlNum.c
CNEr/src/ucsc/sqlNum.h
CNEr/src/ucsc/udc.c
CNEr/src/ucsc/udc.h
CNEr/src/ucsc/verbose.c
CNEr/src/ucsc/verbose.h
CNEr/src/ucsc/wildcmp.c
CNEr/src/utils.c
CNEr/tests
CNEr/tests/testthat
CNEr/tests/testthat.R
CNEr/tests/testthat/test_Axt.R
CNEr/tests/testthat/test_CNE.R
CNEr/tests/testthat/test_GRBs.R
CNEr/tests/testthat/test_GRangePairs.R
CNEr/tests/testthat/test_IO.R
CNEr/tests/testthat/test_ceScan.R
CNEr/tests/testthat/test_reverseCigar.R
CNEr/vignettes
CNEr/vignettes/CNEr.Rmd
CNEr/vignettes/CNEr.bib
CNEr/vignettes/PairwiseWholeGenomeAlignment.Rmd

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