To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("sigaR")
In most cases, you don't need to download the package archive at all.
sigaR
statistics for integrative genomics analyses in R
Bioconductor version: 3.0
Facilites the joint analysis of high-throughput data from multiple molecular levels. Contains functions for manipulation of objects, various analysis types, and some visualization.
Author: Wessel N. van Wieringen <w.vanwieringen at vumc.nl>
Maintainer: Wessel N. van Wieringen <w.vanwieringen at vumc.nl>
Citation (from within R,
enter citation("sigaR")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("sigaR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("sigaR")
| R Script | sigaR | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, GeneExpression, Microarray, Pathways, Software, aCGH |
| Version | 1.10.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) |
| License | GPL (>= 2) |
| Depends | Biobase, CGHbase, methods, mvtnorm, penalized |
| Imports | corpcor (>= 1.6.2), graphics, igraph, marray, MASS, mvtnorm, quadprog, penalized (>= 0.9-39), snowfall, stats |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | http://www.few.vu.nl/~wvanwie |
| Depends On Me | HCsnip |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | sigaR_1.10.0.tar.gz |
| Windows Binary | sigaR_1.10.0.zip |
| Mac OS X 10.6 (Snow Leopard) | sigaR_1.10.0.tgz |
| Mac OS X 10.9 (Mavericks) | sigaR_1.10.0.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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