Registration Open for Bioc2024 July 24-26


fastseg - a fast segmentation algorithm

Bioconductor version: Release (3.19)

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 [aut], Sonali Kumari [ctb], Alexander Blume [cre]

Maintainer: Alexander Blume <alex.gos90 at>

Citation (from within R, enter citation("fastseg")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

An R Package for fast segmentation HTML R Script
Reference Manual PDF


biocViews Classification, CopyNumberVariation, Software
Version 1.50.0
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, grDevices, stats, BiocGenerics, S4Vectors, IRanges
System Requirements
See More
Suggests DNAcopy, oligo, BiocStyle, knitr
Linking To
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_1.50.0.tar.gz
Windows Binary
macOS Binary (x86_64) fastseg_1.50.0.tgz
macOS Binary (arm64) fastseg_1.50.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats