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
Version1.10.1
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

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

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