CNEr

DOI: 10.18129/B9.bioc.CNEr    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see CNEr.

CNE Detection and Visualization

Bioconductor version: 3.11

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>

Installation

To install this package, start R (version "4.0") and enter:

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

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")

 

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

Details

biocViews	DataImport, GeneRegulation, Software, Visualization
Version	1.24.0
In Bioconductor since	BioC 2.14 (R-3.1) (6.5 years)
License	GPL-2 | file LICENSE
Depends	R (>= 3.4)
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
SystemRequirements
Enhances
URL	https://github.com/ge11232002/CNEr
BugReports	https://github.com/ge11232002/CNEr/issues
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_1.24.0.tar.gz
Windows Binary	CNEr_1.24.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	CNEr_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CNEr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CNEr
Package Short Url	https://bioconductor.org/packages/CNEr/
Package Downloads Report	Download Stats