CrypticIBDcheck 0.3-3 – Identifying Cryptic Relatedness in Genetic Association Studies

CrypticIBDcheck 0.3-3

:: DESCRIPTION

CrypticIBDcheck can be used to identify pairs of closely-related subjects based on genetic marker data from single-nucleotide polymorphisms (SNPs). The package is able to accommodate SNPs in linkage disequibrium (LD), without the need to thin the markers so that they are approximately independent in the population. Sample pairs are identified as related by superposing their estimated identity-by-descent (IBD) coefficients on plots of IBD coefficients for pairs of simulated subjects from one of several common close relationships.

::DEVELOPER

Graham & McNeney Labs

: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CrypticIBDcheck

:: MORE INFORMATION

Citation

Source Code Biol Med. 2013 Feb 6;8(1):5. doi: 10.1186/1751-0473-8-5.
CrypticIBDcheck: an R package for checking cryptic relatedness in nominally unrelated individuals.
Nembot-Simo A, Graham J, McNeney B.

SecureMA 0.2 – Secure Meta-analysis for Genetic Association Studies

SecureMA 0.2

:: DESCRIPTION

SecureMA is a secure framework for performing multi-site genetic association studies across large consortia, without violating privacy/confidentiality of individual participants or substudy sites. It aims at addressing various attacks on genomic privacy, and provides comprehensive protection over genomic data without impeding scientific endeavor.

::DEVELOPER

Wei Xie (XieConnect@gmail.com)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 SecureMA

:: MORE INFORMATION

Citation

SecureMA: protecting participant privacy in genetic association meta-analysis.
Xie W, Kantarcioglu M, Bush WS, Crawford D, Denny JC, Heatherly R, Malin BA.
Bioinformatics. 2014 Aug 21. pii: btu561.

FunciSNP 1.32.0 – Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs

FunciSNP 1.32.0

:: DESCRIPTION

FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in coding or non-coding regions.

::DEVELOPER

FunciSNP  team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 FunciSNP

:: MORE INFORMATION

Citation

FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs.
Coetzee SG, Rhie SK, Berman BP, Coetzee GA, Noushmehr H.
Nucleic Acids Res. 2012 Oct;40(18):e139. doi: 10.1093/nar/gks542.