CNEr

This is thedevelopment version of CNEr; for the stable release version, seeCNEr.

CNE Detection and Visualization

DOI: 10.18129/B9.bioc.CNEr

Bioconductor version: Development (3.23)

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

Author: Ge Tan <ge_tan at live.com>

Maintainer: Boris Lenhard <b.lenhard at imperial.ac.uk> Damir Baranasic <damir.baranasic at lms.mrc.ac.uk>

Citation (from within R, entercitation("CNEr")):

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))    install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("CNEr")

For older versions of R, please refer to the appropriateBioconductor 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport,GeneRegulation,Software,Visualization
Version	1.47.0
In Bioconductor since	BioC 2.14 (R-3.1) (11.5 years)
License	GPL-2 \| fileLICENSE
Depends	R (>= 3.5.0)
Imports	Biostrings(>= 2.33.4),pwalign,DBI (>= 0.7),RSQLite (>= 0.11.4),GenomeInfoDb(>= 1.1.3),GenomicRanges(>= 1.23.16),Seqinfo(>= 0.99.2),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)
System Requirements
URL	https://github.com/ComputationalRegulatoryGenomicsICL/CNEr
Bug Reports	https://github.com/ge11232002/CNEr/issues

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
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source Package	CNEr_1.47.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
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

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