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GLAD / Gain and Loss Analysis of DNA
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 Weights Smoothing (AWS) procedure and provides highly convincing results: our algorithm detects 97, 100 and 94% of breakpoints in simulated data, karyotyping results and manually analyzed profiles, respectively. The percentage of correctly assigned statuses ranges from 98.9 to 99.8% for simulated data and is 100% for karyotyping results.
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 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level.
FACADE / Fast Algorithm for Calling After Detection of Edges
Obsolete
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 established algorithms. This is accomplished by utilizing edge detection in combination with non-parametric statistics. Additionally, FACADE requires no specialized knowledge from the user, or complex software environments. FACADE is designed to handle the next generation high-resolution copy number platforms due to the linear scalability of the algorithm. FACADE fills the need, in both research and clinical settings, for rapid accurate segmentation demanded by high-resolution array platforms, large data sets and other situations where long execution times are not tolerable.
aCGH-Smooth
Obsolete
Serves for the automated identification of breakpoints and smoothing of microarray comparative genomic hybridization (array CGH) data. aCGH-Smooth is a program that detects potential breakpoints and smooths the observed array CGH values between consecutive breakpoints to a suitable common value. This tool allows users to adapt the settings for smoothing and breakpoint recognition to the requirements of the raw data, depending on the biological and technical quality of the samples analyzed.
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