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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("pdInfoBuilder")
In most cases, you don't need to download the package archive at all.
pdInfoBuilder
Platform Design Information Package Builder
Bioconductor version: 3.0
Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg.
Author: Seth Falcon, Vince Carey, Matt Settles, Kristof de Beuf, Benilton Carvalho
Maintainer: Benilton Carvalho <beniltoncarvalho at gmail.com>
Citation (from within R,
enter citation("pdInfoBuilder")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("pdInfoBuilder")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("pdInfoBuilder")
| R Script | Building Annotation Packages with pdInfoBuilder for Use with the oligo Package | |
| R Script | PDInfo Package Building Affymetrix Mapping Chips | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Annotation, Infrastructure, Software |
| Version | 1.30.6 |
| In Bioconductor since | BioC 2.0 (R-2.5) |
| License | Artistic-2.0 |
| Depends | R (>= 3.1.0), methods, Biobase(>= 2.25.0), RSQLite (>= 1.0.0), affxparser(>= 1.37.2), oligo(>= 1.29.1) |
| Imports | Biostrings(>= 2.33.14), BiocGenerics(>= 0.11.5), DBI (>= 0.3.1), IRanges(>= 1.99.31), oligoClasses(>= 1.27.2), S4Vectors(>= 0.2.5) |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | maqcExpression4plex |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | pdInfoBuilder_1.30.6.tar.gz |
| Windows Binary | pdInfoBuilder_1.30.6.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | pdInfoBuilder_1.30.6.tgz |
| Mac OS X 10.9 (Mavericks) | pdInfoBuilder_1.30.6.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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