This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

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

CNEr

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

CNE Detection and Visualization

Bioconductor version: Development (3.18)

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

Author: Ge Tan <ge_tan at live.com>

Maintainer: Ge Tan <ge_tan at live.com>

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

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("CNEr")

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

Documentation

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

browseVignettes("CNEr")
CNE identification and visualisation HTML R Script
Pairwise whole genome alignment HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DataImport, GeneRegulation, Software, Visualization
Version 1.37.0
In Bioconductor since BioC 2.14 (R-3.1) (9.5 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)
Linking To 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
System Requirements
Enhances
URL https://github.com/ge11232002/CNEr
Bug Reports https://github.com/ge11232002/CNEr/issues
See More
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_1.37.0.tar.gz
Windows Binary CNEr_1.37.0.zip
macOS Binary (x86_64) CNEr_1.37.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/CNEr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CNEr
Bioc Package Browser https://code.bioconductor.org/browse/CNEr/
Package Short Url https://bioconductor.org/packages/CNEr/
Package Downloads Report Download Stats