tilingArray
Transcript mapping with high-density oligonucleotide tiling arrays
Bioconductor version: Release (3.20)
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 <zxu at embl.de>
citation("tilingArray")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tilingArray")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("tilingArray")| 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 | ||
| Segmentation demo | ||
| Supplement. Calculation of the cost matrix | ||
| Reference Manual |
Details
| biocViews | Microarray, OneChannel, Preprocessing, Software, Visualization |
| Version | 1.84.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 19.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.11.0), Biobase, methods, pixmap |
| Imports | strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | davidTiling |
| Imports Me | ADaCGH2 |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | tilingArray_1.84.0.tar.gz |
| Windows Binary (x86_64) | tilingArray_1.84.0.zip |
| macOS Binary (x86_64) | tilingArray_1.84.0.tgz |
| macOS Binary (arm64) | tilingArray_1.84.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/tilingArray |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tilingArray |
| Bioc Package Browser | https://code.bioconductor.org/browse/tilingArray/ |
| Package Short Url | https://bioconductor.org/packages/tilingArray/ |
| Package Downloads Report | Download Stats |