Tag: Family

FBAT v2.05_beta – Family-Based Association Test

FBAT v2.05_beta

:: DESCRIPTION

FBAT is an acronym for Family-Based Association Tests in genetic analyses. Family-based association designs, as opposed to case-control study designs, are particularly attractive, since they test for linkage as well as association, avoid spurious associations caused by admixture of populations, and are convenient for investigators interested in refining linkage findings in family samples.

::DEVELOPER

FBAT-Toolkit Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX /Sun Workstations

:: DOWNLOAD

FBAT

:: MORE INFORMATION

Citation

Eur J Hum Genet. 2001 Apr;9(4):301-6.
The family based association test method: strategies for studying general genotype–phenotype associations.
Horvath S1, Xu X, Laird NM.

MML – Haplotyping using both Family and Population Infomation

MML

:: DESCRIPTION

MML (Mendalian Constrained Maximum Likelihood) is a software to analyze haplotype polymorphisms in a real human population.

::DEVELOPER

Xin Li 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 MML

:: MORE INFORMATION

Citation

Xin Li, Yixuan Chen and Jing Li.
Detecting Genome-wide Haplotype Polymorphism by Combined Use of Mendelian Constraints and Local Population Structure.
Pacific Symposium on Biocomputing 15:348-358(2010).

APL-OSA Beta – Identify Genetically Homogenous Subset of Families

APL-OSA Beta

:: DESCRIPTION

APL-OSA can identify a genetically homogenous subset of families based on a trait-related covariate. APL-OSA then tests the relationship between the association statistics (i.e., the APL statistics) calculated based on the subset and the family-specific covariate. APL-OSA is based on the OSA method for linkage (Hauser et al. 2004) and the family-based association test, APL (Martin et al. 2003; Chung et al. 2006). Thus, APL-OSA has similar properties with OSA and APL. Bi-alleleic markers such as SNPs are accepted by APL-OSA. APL-OSA is a single-marker test and considers one covariate each time.

::DEVELOPER

Duke Molecular Physiology Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

  APL-OSA

:: MORE INFORMATION

Citation

RH Chung, S Schmidt, ER Martin, ER Hauser.
“Ordered-subset analysis (OSA) for family-based association mapping of complex traits..”
Genetic epidemiology 32.7 (November, 2008): 627-37.

miRClassify 1.0 – miRNA Family Classification and Annotation

miRClassify 1.0

:: DESCRIPTION

miRClassify is a novel machine learning-based web server which can rapidly identify miRNA from the primary sequence and classify it into a miRNA family in regardless of similarity in sequence and structure.

::DEVELOPER

Data Mining Group, Xiamen University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JAVA
  • Apache-Tomcat

:: DOWNLOAD

 miRClassify

:: MORE INFORMATION

Citation

Quan Zou*, Yaozong Mao, Lingling Hu, Yunfeng Wu, Zhiliang Ji*.
miRClassify: An advanced web server for miRNA family classification and annotation.
Computers in Biology and Medicine. 2014, 45:157-160.

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.

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.

LKM 2.0 / LFKM 2.0 / MFKM 1.1 – Quantitative Traits in Longitudinal ( Multivariate) (Family) Data

LKM 2.0 / LFKM 2.0 / MFKM 1.1

:: DESCRIPTION

LKM / LFKM / MFKM is an R package of gene based kernel machine regression for quantitative traits in longitudinal (Multivariate) (Family) Data.

::DEVELOPER

Qi Yan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
:: DOWNLOAD

LKM / LFKM / MFKM

:: MORE INFORMATION

Citation

Yan Q, Weeks DE, Tiwari HK, Yi N, Zhang K, Gao G, Lin WY, Lou XY, Chen W, Liu N.
Rare-Variant Kernel Machine Test for Longitudinal Data from Population and Family Samples.
Hum Hered. 2015;80(3):126-38. doi: 10.1159/000445057. Epub 2016 Apr 29. PMID: 27161037; PMCID: PMC4940283.

Yan Q, Weeks DE, Celedón JC, Tiwari HK, Li B, Wang X, Lin WY, Lou XY, Gao G, Chen W, Liu N.
Associating Multivariate Quantitative Phenotypes with Genetic Variants in Family Samples with a Novel Kernel Machine Regression Method.
Genetics. 2015 Dec;201(4):1329-39. doi: 10.1534/genetics.115.178590. Epub 2015 Oct 19. PMID: 26482791; PMCID: PMC4676518.

FamAgg 1.21.2 – Pedigree Analysis and Familial Aggregation

FamAgg 1.21.2

:: 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

Eurac Biomedical Research

:: 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.

FGAP 060302 – Family Genotype Analysis Program

FGAP 060302

:: DESCRIPTION

FGAP can be used to detect association between a disease and a diallelic polymorphism of a candidate gene by analyzing genotypes in arbitrary types of nuclear families.

:: DEVELOPER

Epidemiology & Population Health, Stanford University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • Java

:: DOWNLOAD

 FGAP

:: MORE INFORMATION

Citation

Genet Epidemiol. 2002 Feb;22(2):128-45.
Tests for genetic association using family data.
Shih MC1, Whittemore AS.

DomStratStats v1.05 – Compute per-protein Domain Family q-values and local FDRs

DomStratStats v1.05

:: 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.