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Segmentation software tools | Genomic array data analysis

Array Comparative Genomic Hybridization (aCGH) is used to scan the entire genome for variations in DNA copy number. A central task in the analysis of aCGH data is the segmentation into groups of probes sharing the same DNA copy number.Source…
DNAcopy
Desktop

DNAcopy

DNA copy number data analysis. DNAcopy segments DNA copy number data using…

DNA copy number data analysis. DNAcopy segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number.

GLAD
Desktop

GLAD Gain and Loss Analysis of DNA

A package for the automatic detection of breakpoints from array CGH profile,…

A package for the automatic detection of breakpoints from array CGH profile, and the assignment of a status to each chromosomal region. The breakpoint detection step of GLAD is based on the Adaptive…

ADaCGH
Desktop
Web

ADaCGH Analysis of Data from aCGH

A web tool for the analysis of aCGH data sets. ADaCGH is a package that…

A web tool for the analysis of aCGH data sets. ADaCGH is a package that parallelizes the main segmentation algorithms (using forking on multicore computers or parallelization via message passing…

HMMSeg
Desktop

HMMSeg

A program for the scale-specific segmentation of continuous genomic data using…

A program for the scale-specific segmentation of continuous genomic data using hidden Markov models (HMMs).

CGHseg
Desktop

CGHseg

An R package dedicated to the analysis of CGH profiles using segmentation…

An R package dedicated to the analysis of CGH profiles using segmentation models. CGHseg implements a dynamic programming algorithm for break point positioning, as well as a model selection criterion…

HaarSeg
Desktop

HaarSeg

A segmentation method based on wavelet decomposition and thresholding, which…

A segmentation method based on wavelet decomposition and thresholding, which detects significant breakpoints in the data.

jointseg
Desktop

jointseg

This package implements functions to quickly segment multivariate signals into…

This package implements functions to quickly segment multivariate signals into piecewise constant profiles and a framework to generate realistic copy-number profiles.

iSeg
Desktop

iSeg

Permits user to work on segmentation of genomic and epigenomic profiles. iSeg…

Permits user to work on segmentation of genomic and epigenomic profiles. iSeg uses both simulated and experimental data and can detect segments of any length. Moreover, it can detect candidate…

Segmentor3IsBac…
Desktop

Segmentor3IsBack

Performs a fast exact segmentation on data. Segmentor3IsBack is a framework…

Performs a fast exact segmentation on data. Segmentor3IsBack is a framework package that allows the use of various cost functions. It exacts change-point algorithm for the segmentation of profiles…

PSCBS
Desktop

PSCBS

Segmentation of allele-specific DNA copy number data and detection of regions…

Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome.

Copynumber
Desktop

Copynumber

Offers a unified framework for single sample, multi-sample and multi-track…

Offers a unified framework for single sample, multi-sample and multi-track segmentation and is based on statistically sound penalized least squares principles. Conditional on the number of…

SegAnnDB
Web

SegAnnDB

Improves previous visualization approaches by allowing the model to be…

Improves previous visualization approaches by allowing the model to be interactively updated using annotated regions. SegAnnDB is a Web-based computer vision system for DNA copy number profile…

CnaStruct
Desktop

CnaStruct

A bivariate segmentation method designed for allele-specific copy number…

A bivariate segmentation method designed for allele-specific copy number analysis on SNP arrays.

CINdex
Desktop

CINdex

Addresses important area of high-throughput genomic analysis. The CINdex…

Addresses important area of high-throughput genomic analysis. The CINdex package allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0…

snapCGH
Desktop

snapCGH

A package based on methods for segmenting, normalising and processing aCGH…

A package based on methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays.

cghMCR
Desktop

cghMCR

This package provides functions to identify genomic regions of interests based…

This package provides functions to identify genomic regions of interests based on segmented copy number data from multiple samples.

BioHMM
Desktop

BioHMM

A method for segmenting array comparative genomic hybridization data into…

A method for segmenting array comparative genomic hybridization data into states with the same underlying copy number. By utilizing a heterogeneous hidden Markov model, BioHMM incorporates relevant…

CRP_LOH
Desktop

CRP_LOH

A LOH inference and segmentation algorithm based on the conditional random…

A LOH inference and segmentation algorithm based on the conditional random pattern (CRP) model. The model explicitly considers the distance between two neighboring SNPs, as well as the genotyping…

Rseg
Desktop

Rseg

An R package to optimize segmentation of SNP array data.

An R package to optimize segmentation of SNP array data.

FACADE
Desktop

FACADE Fast Algorithm for Calling After Detection of Edges

A rapid segmentation and calling algorithm that performs competitively with…

A rapid segmentation and calling algorithm that performs competitively with other popular algorithms, while demonstrating rapid execution times which can be orders of magnitude faster than…

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