CNEr
This is the development version of CNEr; for the stable release version, see CNEr.
CNE Detection and Visualization
Bioconductor version: Development (3.21)
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 "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, GeneRegulation, Software, Visualization |
| Version | 1.43.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10.5 years) |
| License | GPL-2 | file LICENSE |
| Depends | R (>= 3.5.0) |
| Imports | Biostrings(>= 2.33.4), pwalign, DBI (>= 0.7), RSQLite (>= 0.11.4), 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_1.43.0.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 |