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Bash Package MitoDel : Detection of Long Mitochondrial Deletions at Low Heteroplasmy



MitoDel: A Method to Detect and Quantify Mitochondrial DNA Deletions from Next-Generation Sequence Data (Submitted).

Download MitoDel source code here

Java source code DB2 : Distribution Based detection of Duplication Boundaries



DB2: A Probabilistic Approach for Accurate Detection of Tandem Duplication Breakpoints Using Paired-End Reads (Yavas et al., BMC Genomics 2014).

Download DB2 package Java source code here

Download DataGen package Java source code that generates NGS paired-end data with different types of randomly created structural variation by modifying a user-provided chromosome here

R package HWELOH : Hardy-Weinberg Disequilibrium based method of calling LOH



Losing Balance: Hardy-Weinberg Disequilibrium as a Marker for Recurrent Loss-of-Heterozygosity in Cancer (Wilkins and LaFramboise, Human Molecular Genetics 2011).

Download HWELOH package source (UNIX) here


R package COKGEN : CNV Identification using Objective Function Optimization from Affymetrix 6.0 Array Data



An Optimization Framework for Unsupervised Identification of Rare Copy Number Variation from SNP Array Data (Yavas et al., Genome Biology 2009).

Download COKGEN package source (UNIX) here

Download COKGEN package for Windows here

Requires affxparser (>= 1.12.2) package from Bioconductor and numDeriv package from CRAN

Download an example HapMap .CEL file to use with COKGEN package here


R package RankCopy : Nonparametric Methods to Detect Copy Number Variation



Containing rank-based methods to detect copy number change from raw array data (LaFramboise et al., Bioinformatics 2009).

Download RankCopy package source (UNIX) here

Download RankCopy package for Windows here


R package PLASQ : Probe-Level Allele-specific Quantitation



Containing methods to find allele- and parent-specific copy numbers from 100K SNP array data

Requires affy and GLAD packages from Bioconductor as well as aws package from CRAN

Download PLASQ package source (UNIX) here

Download PLASQ package for Windows here

A rough outline giving instructions on how to use PLASQ in its most basic form may be found here.

NEW (28/6/06)!!! PLASQ is now available for 10K array data. Thanks to Jacob Zhang of the Van Andel Institute. Download code here and documentation here.

NEW (27/10/06)!!! PLASQ500K now available, for Affymetrix 500K and 250K platform.
Download PLASQ500K package source (UNIX) here

Download PLASQ500K package for Windows here

Information about R and use of its packages may be found here