DeepGS 1.2 – Predicting Phenotypes from Genotypes using Deep Learning

DeepGS 1.2

:: DESCRIPTION

DeepGS is a R package for predicting phenotypes from genotypes using deep learning techniques.

::DEVELOPER

Ma Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

DeepGS

:: MORE INFORMATION

Citation

Ma W, Qiu Z, Song J, Li J, Cheng Q, Zhai J, Ma C.
A deep convolutional neural network approach for predicting phenotypes from genotypes.
Planta. 2018 Nov;248(5):1307-1318. doi: 10.1007/s00425-018-2976-9. Epub 2018 Aug 12. PMID: 30101399.

SXTestPlate 1.0.0 – Analyses Genotypes of a SNPlex™ Control Plate

SXTestPlate 1.0.0

:: DESCRIPTION

SXTestPlate is a Windows program for evaluating the performance of a SNPlex™ genotyping platform by analyzing a test plate, which was typed with a control pool.

::DEVELOPER

Institute for Clinical Molecular Biology

:: SCREENSHOTS

::REQUIREMENTS

  • Windows
  • Microsoft SQL Server

:: DOWNLOAD

 SXTestPlate

:: MORE INFORMATION

Citation

Teuber M, Wenz MH, Schreiber S, Franke A (2009).
GMFilter and SXTestPlate: software tools for improving the SNPlex(TM) genotyping system.
BMC Bioinformatics 10(1):81

COLONY 2.0.6.7 – Parentage and Sibship Inference from Multilocus Genotype data

COLONY 2.0.6.7

:: DESCRIPTION

COLONY is a Fortran program that implements a maximum likelihood method to assign sibship and parentage jointly, using individual multilocus genotypes at a number of codominant or dominant marker loci.

:: DEVELOPER

Dr Jinliang Wang

:: SCREENSHOTS

COLONY

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

 COLONY

:: MORE INFORMATION

Citation

Jones, O. and Wang, J. (2009)
COLONY: a program for parentage and sibship inference from multilocus genotype data.
Molecular Ecology Resources 10: 551–555.

Wang, J. (2012)
Computationally efficient sibship and parentage assignment from multilocus marker data.
Genetics 191: 183-194.

FISH 0.2 – Fast Genotype Imputation with Segmental Hidden Markov model.

FISH 0.2

:: DESCRIPTION

FISH is a java program for fast and accurate diploid genotype imputation.

::DEVELOPER

Dr. Lei Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 FISH

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 31. [Epub ahead of print]
FISH: fast and accurate diploid genotype imputation via segmental hidden Markov model.
Zhang L1, Pei YF, Fu X, Lin Y, Wang YP, Deng HW.

GenoExp v1 – Gene Expression Prediction from Genotype

GenoExp v1

:: DESCRIPTION

GenoExp is a web tool for predicting gene expression levels from single nucleotide polymorphisms.

::DEVELOPER

Segal Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Matlab

:: DOWNLOAD

 GenoExp

:: MORE INFORMATION

Citation:

Bioinformatics. 2015 Jan 30. pii: btv050.
GenoExp: A web tool for predicting gene expression levels from single nucleotide polymorphisms.
Manor O1, Segal E

SIMLAPLOT 1.0 – Visualize Genotype and Phenotype Relationship

SIMLAPLOT 1.0

:: DESCRIPTION

SIMLAPLOT is a software for visualizing different ways in which continuous covariates may influence the genotype-specific risk for complex human diseases. The purpose of our study was to examine continuous covariates in the Genetic Analysis Workshop 15 simulated data set using our novel graphical display tool, with knowledge of the answers. The generated plots provide information about genetic models for the simulated continuous covariates and may help identify the single-nucleotide polymorphisms associated with the underlying quantitative trait loci.

::DEVELOPER

Duke Molecular Physiology Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SIMLAPLOT

:: MORE INFORMATION

Citation

Xuejun Qin,et al
Visualizing genotype × phenotype relationships in the GAW15 simulated data
BMC Proc. 2007; 1(Suppl 1): S132.

PedPhase 3.0 – Haplotype Inference from Genotypes on Pedigree data

PedPhase 3.0

:: DESCRIPTION

PedPhase is a suite of computer programs for haplotype inference from genotypes on pedigree data. It consists of several different algorithms that are designed based on a combinatorial formulation of haplotype inference, namely the minimum-recombinant haplotype configuration (MRHC) problem, and are effective for different types of data.

::DEVELOPER

Computational Biology lab @ Case (CBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 PedPhase

:: MORE INFORMATION

Citation

Li X, Li J.
An almost linear time algorithm for a general haplotype solution on tree pedigrees with no recombination and its extensions.
J Bioinform Comput Biol. 2009 Jun;7(3):521-45.

HAPSIM – Produce the Case-control Multilocus Genotype Data

HAPSIM

:: DESCRIPTION

HAPSIM is a program for generating case-control multi-locus genotype data under a specified disease model.

::DEVELOPER

Bernard North

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

HAPSIM

:: MORE INFORMATION

Citation:

B.V. North, D. Curtis, P.G.Cassell, G.A.Hitman and P. C. Sham
Assessing optimal neural network architecture for identifying disease-associated multi-marker genotypes using a permutation test, and application to calpain 10 polymorphisms associated with diabetes.
Annals of Human Genetics 67: 348-356

NNPERM 1.3 – Analyse Case-control Multi-locus Genotype Data

NNPERM 1.3

:: DESCRIPTION

NNPERM is a neural network program for analysing case-control multi-locus genotype data using a permutation test.

::DEVELOPER

Bernard North

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

NNPERM

:: MORE INFORMATION

Citation:

B.V. North, D. Curtis, P.G.Cassell, G.A.Hitman and P. C. Sham
Assessing optimal neural network architecture for identifying disease-associated multi-marker genotypes using a permutation test, and application to calpain 10 polymorphisms associated with diabetes.
Annals of Human Genetics 67: 348-356