CNEr

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14

CNE Detection and Visualization

Bioconductor version: Development (3.24)

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, enter citation("CNEr")):

Ge Tan. CNEr: CNE Detection and Visualization. doi:10.18129/B9.bioc.CNEr, R package version 1.49.1, https://bioconductor.org/packages/CNEr.

Generated from the package metadata; it may differ from the package's own citation.

Installation

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

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, GeneRegulation, Software, Visualization
Version	1.49.1
In Bioconductor since	BioC 2.14 (R-3.1) (12.5 years)
License	GPL-2 \| file LICENSE
Depends	R (>= 3.5.0)
Imports	Biostrings (>= 2.33.4), pwalign, DBI (>= 0.7), RSQLite (>= 0.11.4), GenomicRanges (>= 1.23.16), Seqinfo (>= 0.99.2), rtracklayer (>= 1.25.5), XVector (>= 0.5.4), cigarillo, 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, r-universe

Package Archives

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

Source Package	CNEr_1.49.1.tar.gz
Windows Binary (x86_64)	CNEr_1.49.1.zip (64-bit only)
macOS Binary (big-sur-x86_64)	CNEr_1.49.1.tgz
macOS Binary (sonoma-arm64)
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