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CNEr

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

CNE Detection and Visualization


Bioconductor version: Development (3.19)

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 "4.4") 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 1.39.0
In Bioconductor since BioC 2.14 (R-3.1) (10 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)
System Requirements
URL https://github.com/ge11232002/CNEr
Bug Reports https://github.com/ge11232002/CNEr/issues
See More
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 TFBSTools
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package CNEr_1.39.0.tar.gz
Windows Binary CNEr_1.39.0.zip (64-bit only)
macOS Binary (x86_64) CNEr_1.39.0.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