CNEr: CNE Detection and Visualization

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

Author
Ge Tan <ge.tan09@imperial.ac.uk>
Date of publication
None
Maintainer
Ge Tan <ge.tan09@imperial.ac.uk>
License
GPL-2 | file LICENSE
Version
1.10.1
URLs

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

Files in this package

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