To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("PREDA")
In most cases, you don't need to download the package archive at all.
PREDA
Position RElated Data Anlysis
Bioconductor version: 3.0
Package for the position related analysis of quantitative functional genomics data.
Author: Francesco Ferrari <francesco.ferrari at unimore.it>
Maintainer: Francesco Ferrari <francesco.ferrari at unimore.it>
Citation (from within R,
enter citation("PREDA")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("PREDA")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("PREDA")
| R Script | PREDA S4-classes | |
| R Script | PREDA tutorial | |
| Reference Manual |
Details
| biocViews | CopyNumberVariation, GeneExpression, Genetics, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | GPL-2 |
| Depends | R (>= 2.9.0), Biobase, lokern (>= 1.0.9), multtest, stats, methods, annotate |
| Imports | |
| LinkingTo | |
| Suggests | quantsmooth, qvalue, samr, limma, caTools, affy, PREDAsampledata |
| SystemRequirements | |
| Enhances | Rmpi, rsprng |
| URL | |
| Depends On Me | PREDAsampledata |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | PREDA_1.12.0.tar.gz |
| Windows Binary | PREDA_1.12.0.zip |
| Mac OS X 10.6 (Snow Leopard) | PREDA_1.12.0.tgz |
| Mac OS X 10.9 (Mavericks) | PREDA_1.12.0.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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