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Normalization software tools | Genomic array data analysis

Array-based comparative genomic hybridization (array-CGH) is a recently developed technique for analyzing changes in DNA copy number. As in all microarray analyses, normalization is required to correct for experimental artifacts while preserving the…
CGHnormaliter
Desktop

CGHnormaliter

Offers a sophisticated normalization of aCGH data. CGHnormaliter is a method…

Offers a sophisticated normalization of aCGH data. CGHnormaliter is a method that eliminates the ‘overnormalizing’ effect of copy number alterations (CNAs) as well as largescale copy number…

ITALICS
Desktop

ITALICS

A package based on a normalization method that estimates both biological and…

A package based on a normalization method that estimates both biological and nonrelevant effects in an alternate, iterative manner, accurately eliminating irrelevant effects. ITALICS uses a…

MANOR
Desktop

MANOR CGH Micro-Array NORmalization

A package based on an automatic method for the spatial normalization of…

A package based on an automatic method for the spatial normalization of array-CGH data. This method makes it possible to delineate and to eliminate and/or correct areas affected by spatial bias. It…

tQN
Desktop

tQN

A strategy using quantile normalization to improve the quality of data from…

A strategy using quantile normalization to improve the quality of data from Illumina Infinium Whole-Genome Genotyping SNP Beadchips.

aCGH.Spline
Desktop

aCGH.Spline

An efficient, robust normalization method using natural cubic spline…

An efficient, robust normalization method using natural cubic spline interpolation, which consistently removes, in a computationally efficient manner, the dye biases seen across a large range of aCGH…

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.

Ginkgo
Desktop

Ginkgo

A spotted microarray data pre-processing platform featuring analysis…

A spotted microarray data pre-processing platform featuring analysis functionalities for CGH and expression data.

aCGHplus
Desktop

aCGHplus

A method to preprocess comparative genomic hybridization (CGH) bacterial…

A method to preprocess comparative genomic hybridization (CGH) bacterial artificial chromosome (BAC) arrays.

Micro-Analyzer
Desktop

Micro-Analyzer

Java tool that performs the preprocessing of Expression and SNPs microarray…

Java tool that performs the preprocessing of Expression and SNPs microarray Affymetrix.

TumorBoost
Desktop

TumorBoost

A method for normalizing allelic estimates of one tumor sample based on…

A method for normalizing allelic estimates of one tumor sample based on estimates from a single matched normal. TumorBoost increases the power to detect somatic copy-number events (including…

PAIR
Desktop

PAIR Paired Allelic log-Intensity-Ratio

A method to correctly identify two-copy probes from the genome to obtain…

A method to correctly identify two-copy probes from the genome to obtain representative references for normalization in single nucleotide polymorphism arrays. PAIR is based on a two-state Hidden…

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