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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("tilingArray")
In most cases, you don't need to download the package archive at all.
tilingArray
Transcript mapping with high-density oligonucleotide tiling arrays
Bioconductor version: 2.14
The package provides functionality that can be useful for the analysis of high-density tiling microarray data (such as from Affymetrix genechips) for measuring transcript abundance and architecture. The main functionalities of the package are: 1. the class 'segmentation' for representing partitionings of a linear series of data; 2. the function 'segment' for fitting piecewise constant models using a dynamic programming algorithm that is both fast and exact; 3. the function 'confint' for calculating confidence intervals using the strucchange package; 4. the function 'plotAlongChrom' for generating pretty plots; 5. the function 'normalizeByReference' for probe-sequence dependent response adjustment from a (set of) reference hybridizations.
Author: Wolfgang Huber, Zhenyu Xu, Joern Toedling with contributions from Matt Ritchie
Maintainer: Zhenyu Xu <zhenyu at ebi.ac.uk>
Citation (from within R,
enter citation("tilingArray")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("tilingArray")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("tilingArray")
| R Script | Introduction to the plotAlongChrom function | |
| R Script | Introduction to using the segment function to fit a piecewise constant curve | |
| R Script | Normalisation with the normalizeByReference function in the tilingArray package | |
| R Script | Segmentation demo | |
| R Script | Supplement. Calculation of the cost matrix | |
| Reference Manual |
Details
| biocViews | Microarray, OneChannel, Preprocessing, Software, Visualization |
| Version | 1.42.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier |
| License | Artistic-2.0 |
| Depends | R (>= 2.11.0), Biobase, methods, pixmap |
| Imports | strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 |
| Suggests | |
| System Requirements | |
| URL | |
| Depends On Me | davidTiling |
| Imports Me | ADaCGH2, snapCGH |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | tilingArray_1.42.0.tar.gz |
| Windows Binary | tilingArray_1.42.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | tilingArray_1.42.0.tgz |
| Mac OS X 10.9 (Mavericks) | tilingArray_1.42.0.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
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