DoReMi : Donor Recipient Mitochondrial DNA Matching
Mitochondrial Genomics in the Cancer Cell Line Encyclopedia and a Scoring Method to Effectively Pair Cell Lines for Cytoplasmic Hybridization (Grandhi et al, Mitochondrion 2018).
Download DoReMi source code here
MitoDel: Detection of Long Mitochondrial Deletions at Low Heteroplasmy
MitoDel: A Method to Detect and Quantify Mitochondrial DNA Deletions from Next-Generation Sequence Data (Bosworth et al, BMC Bioinformatics 2017).
Download MitoDel source code here
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
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 R package source (UNIX) here
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 R package source (UNIX) here
Download COKGEN R package for Windows here
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 R package source (UNIX) here
Download RankCopy R package for Windows here
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
Download PLASQ R package source (UNIX) here
Download PLASQ R 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 R package for Windows here
Information about R and use of its packages may be found here
Last update on: 28th February 2019