fastseg
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see fastseg.
fastseg - a fast segmentation algorithm
Bioconductor version: 3.9
fastseg implements a very fast and efficient segmentation algorithm. It has similar functionality as DNACopy (Olshen and Venkatraman 2004), but is considerably faster and more flexible. fastseg can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector. Various data formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data. The segmentation criterion of fastseg is based on a statistical test in a Bayesian framework, namely the cyber t-test (Baldi 2001). The speed-up arises from the facts, that sampling is not necessary in for fastseg and that a dynamic programming approach is used for calculation of the segments' first and higher order moments.
Author: Guenter Klambauer
Maintainer: Guenter Klambauer <fastseg at bioinf.jku.at>
citation("fastseg")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("fastseg")
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("fastseg")| fastseg: Manual for the R package | R Script | |
| Reference Manual |
Details
| biocViews | Classification, CopyNumberVariation, Software |
| Version | 1.30.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (12.5 years) |
| License | LGPL (>= 2.0) |
| Depends | R (>= 2.13), GenomicRanges, Biobase |
| Imports | methods, graphics, stats, BiocGenerics, S4Vectors, IRanges |
| System Requirements | |
| URL | http://www.bioinf.jku.at/software/fastseg/fastseg.html |
See More
| Suggests | DNAcopy, oligo |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | methylKit |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | fastseg_1.30.0.tar.gz |
| Windows Binary | fastseg_1.30.0.zip |
| Mac OS X 10.11 (El Capitan) | fastseg_1.30.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/fastseg |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/fastseg |
| Bioc Package Browser | https://code.bioconductor.org/browse/fastseg/ |
| Package Short Url | https://bioconductor.org/packages/fastseg/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |