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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("genomeIntervals")
In most cases, you don't need to download the package archive at all.
genomeIntervals
Operations on genomic intervals
Bioconductor version: 3.0
This package defines classes for representing genomic intervals and provides functions and methods for working with these. Note: The package provides the basic infrastructure for and is enhanced by the package 'girafe'.
Author: Julien Gagneur <gagneur at genzentrum.lmu.de>, Joern Toedling, Richard Bourgon, Nicolas Delhomme
Maintainer: Julien Gagneur <gagneur at genzentrum.lmu.de>
Citation (from within R,
enter citation("genomeIntervals")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("genomeIntervals")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("genomeIntervals")
| R Script | Overview of the genomeIntervals package. | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, Genetics, Infrastructure, Software |
| Version | 1.22.3 |
| In Bioconductor since | BioC 2.4 (R-2.9) |
| License | Artistic-2.0 |
| Depends | R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics(>= 0.10.0) |
| Imports | |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | girafe |
| Imports Me | easyRNASeq |
| Suggests Me | RnaSeqTutorial |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | genomeIntervals_1.22.3.tar.gz |
| Windows Binary | genomeIntervals_1.22.3.zip |
| Mac OS X 10.6 (Snow Leopard) | genomeIntervals_1.22.3.tgz |
| Mac OS X 10.9 (Mavericks) | genomeIntervals_1.22.3.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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