ABC4F 1.0 – Approximate Bayesian Computation for F-statistics

ABC4F 1.0

:: DESCRIPTION

ABC4F (Approximate Bayesian Computation for F-statistics) is a free software that estimates F-statistics using dominant data. The method implemented in ABC4F corrects for the ascertainment biases that characterise AFLP markers.

::DEVELOPER

Laboratoire d’Ecologie Alpine

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  ABC4F

:: MORE INFORMATION

Citation

Foll, M, M.A. Baumont and O.E. Gaggiotti, 2008.
An Approximate Bayesian Computation approach to overcome biases that arise when using AFLP markers to study population structure.
Genetics, 179:927-939.

PriorityPruner 0.1.4 – Prune a list of SNPs, while keeping/selecting SNPs of higher Priority

PriorityPruner 0.1.4

:: DESCRIPTION

PriorityPruner is a software program which can prune a list of SNPs that are in high linkage disequilibrium (LD) with other SNPs in the list, while preferentially keeping/selecting SNPs of higher priority (e.g., the most significant SNPs in a genome-wide association study).

::DEVELOPER

PriorityPruner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Java

:: DOWNLOAD

 PriorityPruner

:: MORE INFORMATION

GxEscanR 2.0.2 – Detect GxE interactions in a Genome-wide Association Study

GxEscanR 2.0.2

:: DESCRIPTION

GxEscan detects GxE Interactions in a Genome-wide Association Study

::DEVELOPER

USC Biostats

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GxEscan

:: MORE INFORMATION

Citation:

Genet Epidemiol. 2013 Sep;37(6):603-13. doi: 10.1002/gepi.21748. Epub 2013 Jul 19.
Finding novel genes by testing G × E interactions in a genome-wide association study.
Gauderman WJ1, Zhang P, Morrison JL, Lewinger JP.

BreakFusion 1.0.1 – Identify Gene Fusions from paired-end RNA-Seq data

BreakFusion 1.0.1

:: DESCRIPTION

BreakFusion is a software that combines the strength of reference alignment followed by read-pair analysis and de novo assembly to achieve a good balance in sensitivity, specificity and computational efficiency.

::DEVELOPER

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 BreakFusion

:: MORE INFORMATION

Citation:

Ken Chen et al.
BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data
Bioinformatics (2012) 28 (14): 1923-1924.

Micro-Checker 2.2.3 – Microsatellite Data Checking Software

Micro-Checker 2.2.3

:: DESCRIPTION

Micro-Checker is a Windows application that checks for microsatellite null alleles and scoring errors. It also provides null allele estimates, and adjusts allele and genotypes frequencies.

::DEVELOPER

Cock van Oosterhout, Bill Hutchinson,Derek Wills and Peter Shipley

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Micro-Checker

:: MORE INFORMATION

Citation

Cock van Oosterhout, Bill Hutchinson,Derek Wills and Peter Shipley
MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data
Molecular Ecology Notes (2004)4, 535–538

snp.plotter 0.5.1 – SNP/haplotype Association and Linkage Disequilibrium plotting package

snp.plotter 0.5.1

:: DESCRIPTION

snp.plotter is an R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot and the ability to plot multiple sets of results simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values.

::DEVELOPER

Augustin Luna, Kristin Nicodemus (email: augustin@mail.nih.gov)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 snp.plotter

:: MORE INFORMATION

Citation

Luna, Nicodemus (2007),
snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package“,
Bioinformatics, 23(6):774-776.

QUANTO 1.2.4 – Computes Sample Size or Power for Association Studies

QUANTO 1.2.4

:: DESCRIPTION

Quanto is a program that computes sample size or power for association studies of genes, environmental factors, gene-environment interaction, or gene-gene interaction. Available study designs for a disease (binary) outcome include the unmatched case-control, matched case-control, case-sibling, case-parent, and case-only designs. Study designs for a quantitative tra it include independent individuals and case parent designs.

::DEVELOPER

The Division of Biostatistics @ usc.edu

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 QUANTO

:: MORE INFORMATION

Citation

Gauderman (2002),
Sample size requirements for matched case-control studies of gene-environment interaction“,
Statistics in Medicine, 21:35-50.

ZygProb – Zygosity Probability Calculation

ZygProb

:: DESCRIPTION

ZygProb processes convenient and accurate zygosity probability calculation.

::DEVELOPER

the Statistical and Genomic Epidemiology Laboratory (SGEL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Twin Res Hum Genet. 2006 Apr;9(2):194-7.
On the probability of dizygotic twins being concordant for two alleles at multiple polymorphic loci.
Nyholt DR.

ssSNPer 20070329 – Identify statistically similar SNPs (ssSNPs) in the HapMap

ssSNPer 20070329

:: DESCRIPTION

ssSNPer is a novel user-friendly web interface that provides easy determination of the number and location of untested HapMap SNPs, in the region surrounding a tested HapMap SNP, which are statistically similar and would thus produce comparable and perhaps more significant association results.

::DEVELOPER

the Statistical and Genomic Epidemiology Laboratory (SGEL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • linux

:: DOWNLOAD

 ssSNPer

:: MORE INFORMATION

Citation

Bioinformatics. 2006 Dec 1;22(23):2960-1. Epub 2006 Oct 12.
ssSNPer: identifying statistically similar SNPs to aid interpretation of genetic association studies.
Nyholt DR.

SNPSpD / SNPSpDlite – Single Nucleotide Polymorphism Spectral Decomposition

SNPSpD / SNPSpDlite

:: DESCRIPTION

SNPSpD is a method of correcting for non-independence of SNPs in LD with each other

SNPSpDlite takes the same input at SNPSpD, but ONLY outputs the LD correlation matrix, Meff and MeffLi estimates and GOLD input (i.e., does not perform time-consuming varimax/promax rotations) thus allowing users to obtain Meff/MeffLi values for large numbers (1000s) of SNPs.

::DEVELOPER

the Statistical and Genomic Epidemiology Laboratory (SGEL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Am J Hum Genet. 2004 Apr;74(4):765-9. Epub 2004 Mar 2.
A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other.
Nyholt DR.