geQTL – Unraveling Group and individual Associations in eQTL Mapping

geQTL

:: DESCRIPTION

geQTL is a sparse regression method that can detect both group-wise and individual associations between SNPs and expression traits.

::DEVELOPER

Wei Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler / MatLab

:: DOWNLOAD

 geQTL

:: MORE INFORMATION

Citation

Sparse regression models for unraveling group and individual associations in eQTL mapping.
Cheng W, Shi Y, Zhang X, Wang W.
BMC Bioinformatics. 2016 Mar 22;17(1):136. doi: 10.1186/s12859-016-0986-9.

LncDisease 1.41 – Predicting lncRNA-disease Associations

LncDisease 1.41

:: DESCRIPTION

LncDisease is a novel computational method and tool to predict the associations between lncRNAs and diseases

::DEVELOPER

the Cui Lab

:: SCREENSHOTS

LncDisease

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 LncDisease

:: MORE INFORMATION

Citation

LncDisease: a sequence based bioinformatics tool for predicting lncRNA-disease associations.
Wang J, Ma R, Ma W, Chen J, Yang J, Xi Y, Cui Q.
Nucleic Acids Res. 2016 Feb 16. pii: gkw093

PC-select – Calculation of GWAS Association Statistics

PC-select

:: DESCRIPTION

PC-select calculates GWAS association statistics using a data-adaptive GRM that improves power over standard mixed models while simultaneously avoiding confounding from population stratification.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PC-select

:: MORE INFORMATION

Citation:

Genetics. 2014 Jul;197(3):1045-9. doi: 10.1534/genetics.114.164285. Epub 2014 Apr 29.
Improving the power of GWAS and avoiding confounding from population stratification with PC-Select.
Tucker G, Price AL, Berger B

rcNet – Web Tool for Inferring Disease and Gene Set Association

rcNet

:: DESCRIPTION

rcNet (Rank Coherence in Networks) web tool provides an online resource to predict associations between disease phenotypes and gene sets. rcNet algorithms combine known disease-gene associations in OMIM with the topological information in the disease phenotype similarity network and the gene-gene interaction network to analyze the association between a gene set and disease phenotypes. The networks provide richer and more reliable information for computing the association scores used to rank the phenotypes. reNet algorithms could be applied to validate and analyze the candidate disease gene identified in GWAS, DNA copy number analysis, and Microarray gene expression profiling.

::DEVELOPER

Kuang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Matlab

:: DOWNLOAD

 rcNet

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Oct 1;27(19):2692-9. doi: 10.1093/bioinformatics/btr463. Epub 2011 Aug 8.
Inferring disease and gene set associations with rank coherence in networks.
Hwang T, Zhang W, Xie M, Liu J, Kuang R.

GWiS 1.1 – a Gene-based Test of Association

GWiS 1.1

:: DESCRIPTION

GWiS (a novel Gene-Wide Significance) test uses greedy Bayesian model selection to identify the independent effects within a gene, which are combined to generate a stronger statistical signal.

::DEVELOPER

Joel Bader lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 GWiS

:: MORE INFORMATION

Citation

PLoS Genet. 2011 Jul;7(7):e1002177. doi: 10.1371/journal.pgen.1002177. Epub 2011 Jul 28.
Gene-based tests of association.
Huang H, Chanda P, Alonso A, Bader JS, Arking DE.

vntrTest 0.52 – Assess Association of VNTR Fragment Length Genotypes

vntrTest 0.52

:: DESCRIPTION

vntrTest is a program for assessing association of VNTR fragment length genotypes with either continuous or case-control outcomes.

::DEVELOPER

Dr Lachlan J Coin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 vntrTest

:: MORE INFORMATION

Citation

Hum Mol Genet. 2012 Aug 15;21(16):3727-38. doi: 10.1093/hmg/dds187.
Novel association approach for variable number tandem repeats (VNTRs) identifies DOCK5 as a susceptibility gene for severe obesity.
El-Sayed Moustafa JS, Eleftherohorinou H, de Smith AJ, Andersson-Assarsson JC, Alves AC, Hadjigeorgiou E, Walters RG, Asher JE, Bottolo L, Buxton JL, Sladek R, Meyre D, Dina C, Visvikis-Siest S, Jacobson P, Sj?str?m L, Carlsson LM, Walley A, Falchi M, Froguel P, Blakemore AI, Coin LJ.

multiMiR 1.0.1 – Integration of microRNA-target Interactions along with their Disease and Drug Associations

multiMiR 1.0.1

:: DESCRIPTION

The R package multiMiR is a comprehensive collection of predicted and validated miRNA-target interactions and their associations with diseases and drugs.

::DEVELOPER

Yuanbin Ru at Windber Research Institute & Katerina Kechris at the University of Colorado Denver.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 multiMiR

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014;42(17):e133. doi: 10.1093/nar/gku631. Epub 2014 Jul 24.
The multiMiR R package and database: integration of microRNA-target interactions along with their disease and drug associations.
Ru Y, Kechris KJ, Tabakoff B, Hoffman P, Radcliffe RA, Bowler R, Mahaffey S, Rossi S, Calin GA, Bemis L, Theodorescu D.

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.

MT-HESS 0.3 – Simultaneous Association Detection in OMICS Datasets

MT-HESS 0.3

:: DESCRIPTION

MT-HESS is a Bayesain hierarchical model that analyses the association between a large set of predictors, e.g. SNPs (single nucleotide polymorphisms), and many responses, e.g. gene expression, in multiple tissues, cells or conditions.

::DEVELOPER

MT-HESS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/  MacOSX

:: DOWNLOAD

 MT-HESS

:: MORE INFORMATION

Citation

MT-HESS: an efficient Bayesian approach for simultaneous association detection in OMICS datasets, with application to eQTL mapping in multiple tissues.
Lewin A, Saadi H, Peters JE, Moreno-Moral A, Lee JC, Smith KG, Petretto E, Bottolo L, Richardson S.
Bioinformatics. 2015 Oct 26. pii: btv568

PAINTOR 2.0 – Integration of Functional and Association data in Fine-mapping Studies

PAINTOR 2.0

:: DESCRIPTION

PAINTOR (Probabilistic Annotation INtegraTOR) is a probabilistic framework that integrates association strength with genomic functional annotation data to improve accuracy in selecting plausible causal variants for functional validation.

::DEVELOPER

Bogdan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PAINTOR

:: MORE INFORMATION

Citation:

Integrating functional data to prioritize causal variants in statistical fine-mapping studies.
Kichaev G, Yang WY, Lindstrom S, Hormozdiari F, Eskin E, Price AL, Kraft P,Pasaniuc B.
PLoS Genet. 2014 Oct 30;10(10):e1004722. doi: 10.1371/journal.pgen.1004722. eCollection 2014.