To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("Risa")
In most cases, you don't need to download the package archive at all.
Risa
Converting experimental metadata from ISA-tab into Bioconductor data structures
Bioconductor version: 3.0
The Investigation / Study / Assay (ISA) tab-delimited format is a general purpose framework with which to collect and communicate complex metadata (i.e. sample characteristics, technologies used, type of measurements made) from experiments employing a combination of technologies, spanning from traditional approaches to high-throughput techniques. Risa allows to access metadata/data in ISA-Tab format and build Bioconductor data structures. Currently, data generated from microarray, flow cytometry and metabolomics-based (i.e. mass spectrometry) assays are supported. The package is extendable and efforts are undergoing to support metadata associated to proteomics assays.
Author: Alejandra Gonzalez-Beltran, Audrey Kauffmann, Steffen Neumann, Gabriella Rustici, ISA Team
Maintainer: Alejandra Gonzalez-Beltran, ISA Team <isatools at googlegroups.com>
Citation (from within R,
enter citation("Risa")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("Risa")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("Risa")
| R Script | Risa: converts experimental metadata from ISA-tab into Bioconductor data structures | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Annotation, DataImport, MassSpectrometry, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) |
| License | LGPL |
| Depends | R (>= 2.0.9), Biobase(>= 2.4.0), methods, Rcpp (>= 0.9.13), biocViews, affy |
| Imports | xcms |
| LinkingTo | |
| Suggests | faahKO(>= 1.2.11) |
| SystemRequirements | |
| Enhances | |
| URL | http://isatab.sourceforge.net/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | Risa_1.8.0.tar.gz |
| Windows Binary | Risa_1.8.0.zip |
| Mac OS X 10.6 (Snow Leopard) | Risa_1.8.0.tgz |
| Mac OS X 10.9 (Mavericks) | Risa_1.8.0.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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