To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("SQUADD")
In most cases, you don't need to download the package archive at all.
SQUADD
Add-on of the SQUAD Software
Bioconductor version: 3.0
This package SQUADD is a SQUAD add-on. It permits to generate SQUAD simulation matrix, prediction Heat-Map and Correlation Circle from PCA analysis.
Author: Martial Sankar, supervised by Christian Hardtke and Ioannis Xenarios
Maintainer: Martial Sankar <martial.sankar at unil.ch>
Citation (from within R,
enter citation("SQUADD")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("SQUADD")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SQUADD")
| R Script | SQUADD package | |
| R Script | SQUADD package | |
| Reference Manual |
Details
| biocViews | GraphAndNetwork, Network, Software, Visualization |
| Version | 1.16.0 |
| In Bioconductor since | BioC 2.7 (R-2.12) |
| License | GPL (>=2) |
| Depends | R (>= 2.11.0) |
| Imports | graphics, grDevices, methods, RColorBrewer, stats, utils |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | http://www.unil.ch/dbmv/page21142_en.html |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | SQUADD_1.16.0.tar.gz |
| Windows Binary | SQUADD_1.16.0.zip |
| Mac OS X 10.6 (Snow Leopard) | SQUADD_1.16.0.tgz |
| Mac OS X 10.9 (Mavericks) | SQUADD_1.16.0.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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