To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("CNEr")
In most cases, you don't need to download the package archive at all.
CNEr
CNE detection and visualization.
Bioconductor version: 3.0
Large-scale identification and advanced visualization of sets of conserved noncoding elements.
Author: Ge Tan <ge.tan09 at imperial.ac.uk>
Maintainer: Ge Tan <ge.tan09 at imperial.ac.uk>
Citation (from within R,
enter citation("CNEr")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("CNEr")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CNEr")
| R Script | CNEr | |
| Reference Manual | ||
| Text | LICENSE |
Details
| biocViews | DataImport, GeneRegulation, Software, Visualization |
| Version | 1.2.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) |
| License | GPL-2 | file LICENSE |
| Depends | R (>= 3.0.2) |
| Imports | Biostrings(>= 2.33.4), RSQLite (>= 0.11.4), GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.17.11), rtracklayer(>= 1.25.5), XVector(>= 0.5.4), DBI (>= 0.2-7), GenomicAlignments(>= 1.1.9), methods, S4Vectors(>= 0.0.4), IRanges(>= 1.99.6) |
| LinkingTo | S4Vectors, IRanges, XVector |
| Suggests | Gviz(>= 1.7.4), RUnit, BiocGenerics |
| SystemRequirements | |
| Enhances | |
| URL | http://ancora.genereg.net/ |
| Depends On Me | |
| Imports Me | TFBSTools |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | CNEr_1.2.0.tar.gz |
| Windows Binary | CNEr_1.2.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | CNEr_1.2.0.tgz |
| Mac OS X 10.9 (Mavericks) | CNEr_1.2.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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