This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see CNEr.

CNE Detection and Visualization

Bioconductor version: 3.18

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

Author: Ge Tan <ge_tan at>

Maintainer: Ge Tan <ge_tan at>

Citation (from within R, enter citation("CNEr")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

CNE identification and visualisation HTML R Script
Pairwise whole genome alignment HTML R Script
Reference Manual PDF


biocViews DataImport, GeneRegulation, Software, Visualization
Version 1.38.0
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License GPL-2 | file LICENSE
Depends R (>= 3.5.0)
Imports Biostrings(>= 2.33.4), DBI (>= 0.7), RSQLite (>= 0.11.4), GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.23.16), rtracklayer(>= 1.25.5), XVector(>= 0.5.4), GenomicAlignments(>= 1.1.9), methods, S4Vectors(>= 0.13.13), IRanges(>= 2.5.27), readr (>= 0.2.2), BiocGenerics, tools, parallel, reshape2 (>= 1.4.1), ggplot2 (>= 2.1.0), poweRlaw (>= 0.60.3), annotate(>= 1.50.0), GO.db(>= 3.3.0), R.utils (>= 2.3.0), KEGGREST(>= 1.14.0)
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Suggests Gviz(>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Ggallus.UCSC.galGal3
Linking To S4Vectors, IRanges, XVector
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Imports Me TFBSTools
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Source Package CNEr_1.38.0.tar.gz
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macOS Binary (x86_64) CNEr_1.38.0.tgz
macOS Binary (arm64)
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Source Repository (Developer Access) git clone
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