CANOES
Lead Investigator(s) Yufeng Shen
A method for calling copy number variants from exome sequencing data with an arbitrary number of reference samples.
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CONDEX (condr)
Lead Investigator(s) Itsik Pe'er
A hidden Markov model for detecting copy number variants in exome sequence data.
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DASH
Lead Investigator(s) Itsik Pe'er
DASH (DASH Associates Shared Haplotypes) is a tool for detecting association to clusters of identity by descent (IBD) segments detected by the Germline software tool.
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GAMToC
Lead Investigator(s) Raul Rabadan
Uses copy number and mutation data from a cohort of patients, for example from TCGA, to find modules of genes with a related mutation pattern.
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Germline
Lead Investigator(s) Itsik Pe'er
An algorithm for discovering long shared segments of identity by descent (IBD) between pairs of (unrelated) individuals in a large population.
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HADiT
Lead Investigator(s) Itsik Pe'er
HADiT (Haplotype Amplification Distortion in Tumors) is a tool for computing and visualizing allelic distortion in tumor SNP data.
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HATS
Lead Investigator(s) Itsik Pe'er
A tool for calling amplified alleles and constructing the amplified haplotype within called tumor amplicons.
HELIOS
Lead Investigator(s) Dana Pe'er
Integrates genomic data from primary tumors with data from functional RNAi screens to pinpoint driver genes within large recurrently amplified regions of DNA.
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HLA-IBD
Lead Investigator(s) Itsik Pe'er
A method for inferring per-locus human leukocyte antigen types using shared segments that are identical by descent (IBD), inferred from genotype data.
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INFOSTIP
Lead Investigator(s) Itsik Pe'er
A tool for selecting individual for sequencing by total information potential, based on GERMLINE output.
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JISTIC
Lead Investigator(s) Dana Pe'er
A tool for analyzing datasets of genome-wide copy number variation to identify driver aberrations in cancer. It is an improvement over the widely used GISTIC algorithm.
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MutaGeneSys
Lead Investigator(s) Itsik Pe'er
Uses genome-wide genotype data to estimate individual disease susceptibility.
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OPERA
Lead Investigator(s) Itsik Pe'er
A tool for power estimation and design of whole-genome resequencing projects aimed at rare variant associations.
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PoolDesign
Lead Investigator(s) Itsik Pe'er
A tool for designing overlapping pools for variant-carrier identification.
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Repertoire
Lead Investigator(s) Yufeng Shen
Scripts for analyzing T cell receptor repertoire sequencing data.
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SAVI
Lead Investigator(s) Raul Rabadan
A program for calling variants in high-throughput sequencing data, particularly paired tumor-normal samples.
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SIXPAC
Lead Investigator(s) Itsik Pe'er
An efficient, scalable search algorithm that finds synergy between pairs of physically unlinked SNPs (genome-wide) in large case-control datasets.
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TARGet
Lead Investigator(s) Raul Rabadan
A light-weight application for reconstructing non-vertical evolutionary histories from sampled genetic sequences using persistent homology, a tool from topological data analysis.
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Xplorigin
Lead Investigator(s) Itsik Pe'er
A tool for parsing population ancestry of admixed individuals.
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Zinfandel
Lead Investigator(s) Itsik Pe'er, Yufeng Shen
A tool for detecting CNVs from low-pass whole genome sequencing data.
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