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source("http://bioconductor.org/biocLite.R")
biocLite("GenomicTuples")
In most cases, you don't need to download the package archive at all.
GenomicTuples
Representation and manipulation of genomic tuples
Bioconductor version: 3.0
GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges Bioconductor package.
Author: Peter Hickey <peter.hickey at gmail.com>, with contributions from Marcin Cieslik
Maintainer: Peter Hickey <peter.hickey at gmail.com>
Citation (from within R,
enter citation("GenomicTuples")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GenomicTuples")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GenomicTuples")
| GenomicTuples: Classes and Methods | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataRepresentation, Infrastructure, Sequencing, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), GenomicRanges(>= 1.17.46), GenomeInfoDb, methods |
| Imports | Rcpp (>= 0.11.2), BiocGenerics, S4Vectors, Biobase |
| LinkingTo | Rcpp |
| Suggests | testthat, knitr, BiocStyle |
| SystemRequirements | |
| Enhances | |
| URL | www.github.com/PeteHaitch/GenomicTuples |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | GenomicTuples_1.0.0.tar.gz |
| Windows Binary | GenomicTuples_1.0.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | GenomicTuples_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | GenomicTuples_1.0.0.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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