LIBFBAT 0.5.1 – C++ library for Family Based Association Testing

LIBFBAT 0.5.1

:: DESCRIPTION

LIBFBAT programming library s robust both to genotyping errors and missing genotypes. The underlying method consists in considering an incomplete data model where the true unobserved genotypes produce the observed one through an explicit genotyping error model.

::DEVELOPER

LIBFBAT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OsX/ Linux
  • C++ Compiler

:: DOWNLOAD

LIBFBAT

:: MORE INFORMATION

Citation

Gregory Nuel, Yousri Slaoui and Vincent Miele,
libfbat: a C++ library for family based association testing,
Proceedings of JOBIM, 2008

3FunMap 1.0 – Full-sib Family Functional Mapping tools

3FunMap 1.0

:: DESCRIPTION

3FunMap is a Windows software that can be used to construct genetic linkage maps and perform functional QTL mapping with molecular markers generated in a full-sib family. For linkage analysis, the software utilizes seven segregation types of markers to estimate the recombination and simultaneously predict the linkage phase between any two markers. It takes heuristic search method for ordering large number of markers of a linkage group by incorporating local ordering methods. Multi-locus linkage phases for the optimal order of each linkage group are predicted based on three-point linkage analysis.

::DEVELOPER

Center for Statistical Genetics, Penn State University

:: SCREENSHOTS

3FunMap

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 3FunMap

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jul 15;27(14):2006-8. doi: 10.1093/bioinformatics/btr306. Epub 2011 May 17.
3FunMap: full-sib family functional mapping of dynamic traits.
Tong C, Wang Z, Zhang B, Shi J, Wu R.

DomStratStats – Compute per-protein Domain Family q-values and local FDRs

DomStratStats

:: DESCRIPTION

DomStratStats computes domain q-values and local FDRs, and tiered q-values (combining HMMER3 domain and sequence data).

::DEVELOPER

Mona Singh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl

:: DOWNLOAD

DomStratStats

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2015 Nov 17;11(11):e1004509. doi: 10.1371/journal.pcbi.1004509. eCollection 2015 Nov.
Beyond the E-Value: Stratified Statistics for Protein Domain Prediction.
Ochoa A, Storey JD, Llinás M, Singh M.

EcMap – Evaluate the size of Families for Linkage analysis

EcMap

:: DESCRIPTION

EcMap is a simulation program that allows users to evaluate the size of their families for linkage analysis. The software simulates homologous recombination and inheritance process based on a Chi-square model simulating physical interference but not chromatid interference. The genetic distance map was obtained from HapMap and reflects average male and female genetic distances for each chromosome

::DEVELOPER

WANLING YANG’S GROUP IN BIOINFORMATICSUniversity of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  EcMap

:: MORE INFORMATION

PEDDY v0.4.3 – Detect Sample Mixups in Family based studies of Disease

PEDDY v0.4.3

:: DESCRIPTION

PEDDY is a software package to identify and facilitate the remediation of such errors via interactive visualizations and reports comparing the stated sex, relatedness, and ancestry to what is inferred from the individual genotypes derived from whole-genome (WGS) or whole-exome (WES) sequencing.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

PEDDY

:: MORE INFORMATION

Citation:

Am J Hum Genet. 2017 Mar 2;100(3):406-413. doi: 10.1016/j.ajhg.2017.01.017. Epub 2017 Feb 9.
Who’s Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy.
Pedersen BS, Quinlan AR.

GCORE 201510 – Fast Family-based Gene-gene Interaction Test

GCORE 201510

:: DESCRIPTION

GCORE is an efficient family-based gene-gene interaction test for trios.

::DEVELOPER

Statistical Genetics and Programming Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GSCORE

:: MORE INFORMATION

Citation

An efficient gene-gene interaction test for genome-wide association studies in trio families.
Sung PY, Wang YT, Yu YW, Chung RH.
Bioinformatics. 2016 Feb 11. pii: btw077.

OPTPDT – Family-based multi-SNP Association Test

OPTPDT

:: DESCRIPTION

OPTPDT (Optimal P-value Threshold Pedigree Disequilibrium Test)is a family-based multi-SNP association test. A variable p-value threshold algorithm is used in the test to select an optimal subset of SNPs that has the strongest association signals.

::DEVELOPER

Statistical Genetics and Programming Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 OPTPDT

:: MORE INFORMATION

Citation

BMC Genomics. 2015 May 15;16:381. doi: 10.1186/s12864-015-1620-3.
A multi-SNP association test for complex diseases incorporating an optimal P-value threshold algorithm in nuclear families.
Wang YT, Sung PY, Lin PL, Yu YW, Chung RH

FamAgg 0.99.9 – Pedigree Analysis and Familial Aggregation

FamAgg 0.99.9

:: DESCRIPTION

FamAgg is an open source R package that contains both established and novel methods to investigate familial aggregation of traits in large pedigrees.

::DEVELOPER

Johannes Rainer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R / BioConductor

:: DOWNLOAD

 FamAgg

:: MORE INFORMATION

Citation

FamAgg: an R Package to Evaluate Familial Aggregation of Traits in Large Pedigrees.
Rainer J, Taliun D, D’Elia Y, Pattaro C, Domingues FS, Weichenberger CX.
Bioinformatics. 2016 Jan 22. pii: btw019.

RVFam 1.1 – Rare Variants Association Analyses with Family Data

RVFam 1.1

:: DESCRIPTION

The RVFam package provides functions to perform single SNP association analyses and gene-based tests for continuous, binary and survival traits against sequencing data (e.g. exome chip) using family data.

::DEVELOPER

Ming-Huei Chen <mhchen at bu.edu> and Qiong Yang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • R

:: DOWNLOAD

  RVFam

:: MORE INFORMATION

Citation:

RVFam: An R Package for Rare Variant Association Analysis with Family Data.
Chen MH, Yang Q.
Bioinformatics. 2015 Oct 27. pii: btv609.

famSKAT-RC 20140725 – Combining Family- and Population-based Imputation data for Association analysis of Rare and common Variants in large Pedigrees

famSKAT-RC 20140725

:: DESCRIPTION

famSKAT-RC is an R scripts to carry out a combined rare- and common-variant gene-based test of association in the presence of related individuals.

::DEVELOPER

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 famSKAT-RC

:: MORE INFORMATION

Citation:

Genet Epidemiol. 2014 Nov;38(7):579-90. doi: 10.1002/gepi.21844. Epub 2014 Aug 1.
Combining family- and population-based imputation data for association analysis of rare and common variants in large pedigrees.
Saad M1, Wijsman EM.