Package: CNEr 1.49.0

Boris Lenhard

CNEr: CNE Detection and Visualization

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

CNEr_1.49.0.tar.gz
CNEr_1.49.0.zip(r-4.7)CNEr_1.49.0.zip(r-4.6)CNEr_1.49.0.zip(r-4.5)
CNEr_1.49.0.tgz(r-4.6-x86_64)CNEr_1.49.0.tgz(r-4.6-arm64)CNEr_1.49.0.tgz(r-4.5-x86_64)CNEr_1.49.0.tgz(r-4.5-arm64)
CNEr_1.49.0.tar.gz(r-4.7-arm64)CNEr_1.49.0.tar.gz(r-4.7-x86_64)CNEr_1.49.0.tar.gz(r-4.6-arm64)CNEr_1.49.0.tar.gz(r-4.6-x86_64)
CNEr_1.49.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
CNEr/json (API)
NEWS

# Install 'CNEr' in R:

install.packages('CNEr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ge11232002/cner/issues

Datasets:

axisTrack - Example data for plotting annotation.
CNEDanRer10Hg38 - CNEHg38DanRer10 and CNEDanRer10Hg38 dataset
cneFinalListDanRer10Hg38 - CneFinalListDanRer10Hg38 dataset
CNEHg38DanRer10 - CNEHg38DanRer10 and CNEDanRer10Hg38 dataset
cpgIslands - Example data for plotting annotation.
grangesPairsForDotplot - GrangesPairsForDotplot
refGenes - Example data for plotting annotation.

On BioConductor:CNEr-1.49.0(bioc 3.24)CNEr-1.48.0(bioc 3.23)

generegulation visualization dataimport

7.76 score 4 stars 40 scripts 5.0k downloads 3 mentions 65 exports 104 dependencies

Last updated from:00483733b6. Checks:3 ERROR, 9 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	440
linux-devel-arm64	WARNING	693
linux-devel-x86_64	WARNING	820
source / vignettes	OK	572
linux-release-arm64	WARNING	699
linux-release-x86_64	WARNING	854
macos-release-arm64	ERROR	466
macos-release-x86_64	WARNING	859
macos-oldrel-arm64	ERROR	609
macos-oldrel-x86_64	WARNING	1077
windows-devel	WARNING	679
windows-release	WARNING	704
windows-oldrel	WARNING	674
wasm-release	OK	405

Exports:Axt axtChain axtInfo binFromCoordRange binRangesFromCoordRange binRestrictionString blatCNE ceScan chainMergeSort chainNetSyntenic chainPreNet CNE CNE12 CNE21 CNEDensity CNEFinal cneMerge CNEMerged fetchChromSizes first fixCoordinates GRangePairs grglist last lastal lastz lavToPsl makeAncoraFiles makeAxtTracks makeCNEDensity makeGRBs matchDistribution N50 N90 netToAxt plotCNEDistribution plotCNEWidth psubAxt queryRanges querySeqs read.rmMask.GRanges read.rmskFasta readAncora readAncoraIntoSQLite readAxt readBed readCNERangesFromSQLite reverseCigar saveCNEToSQLite score scoringMatrix second seqinfo seqnames strand subAxt summary swap symCount syntenicDotplot targetRanges targetSeqs thresholds unique writeAxt

Dependencies:abind annotate AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem cigarillo cli clipr codetools cpp11 crayon curl DBI DelayedArray farver fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 glue GO.db gtable hms httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plyr png poweRlaw pracma prettyunits progress pwalign R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RCurl readr reshape2 restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyselect tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML xtable XVector yaml

CNE identification and visualisation

Ge Tan

Rendered fromCNEr.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2016-08-22
Started: 2015-10-08

Pairwise whole genome alignment

Ge Tan

Rendered fromPairwiseWholeGenomeAlignment.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2016-10-06
Started: 2016-02-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add ancestor GO IDs	addAncestorGO
Example data for plotting annotation.	axisTrack cpgIslands refGenes
Class '"Axt"'	Axt Axt-class c,Axt-method length,Axt-method queryRanges queryRanges,Axt-method querySeqs querySeqs,Axt-method score,Axt-method symCount symCount,Axt-method targetRanges targetRanges,Axt-method targetSeqs targetSeqs,Axt-method [,Axt,ANY,ANY-method
axtChain	axtChain
axtInfo function	axtInfo
UCSC bin indexing system utility functions	binFromCoordRange binRangesFromCoordRange binRestrictionString
Wrapper function of blat for 'CNE' object	blatCNE
ceScan function	ceScan ceScan,Axt-method ceScan,CNE-method
chainMergeSort	chainMergeSort
chainNetSyntenic	chainNetSyntenic
chainPreNet	chainPreNet
Class '"CNE"'	CNE CNE-class CNE12 CNE12,CNE-method CNE21 CNE21,CNE-method CNEFinal CNEFinal,CNE-method CNEMerged CNEMerged,CNE-method thresholds thresholds,CNE-method
CNEHg38DanRer10 and CNEDanRer10Hg38 dataset	CNEDanRer10Hg38 CNEHg38DanRer10
CNEDensity function	CNEDensity CNEDensity,ANY,character,character,missing,missing-method CNEDensity,ANY,missing,character,character,character-method CNEDensity-methods
cneFinalListDanRer10Hg38 dataset	cneFinalListDanRer10Hg38
CNE merge function	cneMerge cneMerge,CNE,missing-method cneMerge,GRangePairs,GRangePairs-method
fetchChromSizes function.	fetchChromSizes
Fix the coordinates in 'Axt' object	fixCoordinates fixCoordinates,Axt-method
GRangePairs objects	c,GRangePairs-method class:GRangePairs coerce,GRangePairs,GRanges-method coerce,GRangePairs,GRangesList-method first,GRangePairs-method GRangePairs GRangePairs-class grglist,GRangePairs-method last last,GRangePairs-method second,GRangePairs-method seqinfo,GRangePairs-method seqnames,GRangePairs-method strand,GRangePairs-method swap swap,GRangePairs-method unique,GRangePairs-method unlist,GRangePairs-method
grangesPairsForDotplot	grangesPairsForDotplot
lastal wrapper	lastal
lastz wrapper	lastz
lavToPsl	lavToPsl
makeAncoraFiles	makeAncoraFiles
makeAxtTracks	makeAxtTracks
Make 'Bed', 'bedGraph' and 'BigWig' files	makeCNEDensity
makeGRBs	makeGRBs
Plot the distribution of matched alignments.	matchDistribution matchDistribution,Axt-method
Assembly statistics.	N50 N90
netToAxt	netToAxt
Fetch mapping from KEGG IDs to Entrez IDs	orgKEGGIds2EntrezIDs
Plot sequential CNE number against CNE genomic location	plotCNEDistribution
Plot the CNE widths distribution	plotCNEWidth
Parallel subset of Axt alignment	psubAxt
Query the CNEData package to fetch the CNEs	queryCNEData
Read a RepeatMasker .out file	read.rmMask.GRanges
Read a soft repeat masked fasta	read.rmskFasta
Read the cne file from Ancora format.	readAncora
Read Ancora legacy CNE format	readAncoraIntoSQLite
Read 'Axt' file	readAxt
Read bed file	readBed
readCNERangesFromSQLite function	readCNERangesFromSQLite
reverseCigar function	reverseCigar
Save CNE to SQLite	saveCNEToSQLite
scoringMatrix	scoringMatrix
Subset an 'Axt' object	subAxt subAxt,Axt,character,integer,integer-method subAxt,Axt,character,missing,missing-method subAxt,Axt,character,numeric,numeric-method subAxt,Axt,GRanges,missing,missing-method subAxt-methods
Utility functions related to Axt alignment	summary summary,Axt-method
Syntenic dotplot	syntenicDotplot syntenicDotplot,Axt-method syntenicDotplot,GRangePairs-method
'writeAxt' function	writeAxt