DOI: 10.18129/B9.bioc.CNEr    

This is the development version of CNEr; for the stable release version, see CNEr.

CNE Detection and Visualization

Bioconductor version: Development (3.17)

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))

# The following initializes usage of Bioc devel


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:



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


biocViews DataImport, GeneRegulation, Software, Visualization
Version 1.35.0
In Bioconductor since BioC 2.14 (R-3.1) (8.5 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)
LinkingTo S4Vectors, IRanges, XVector
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
Depends On Me
Imports Me TFBSTools
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CNEr_1.35.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: