Tag: Reduction

MIDER v2 – Mutual Information Distance and Entropy Reduction

MIDER v2

:: DESCRIPTION

MIDER is a general purpose software tool for inferring network structures. It has been developed with biological networks in mind, but can be applied in other areas.

::DEVELOPER

(Bio)Process Engineering group, IIM-CSIC

:: SCREENSHOTS

MIDER

:: REQUIREMENTS

  • Linux /Windows/MacOsX
  • MatLab

:: DOWNLOAD

 MIDER

:: MORE INFORMATION

Citation

MIDER: Network Inference with Mutual Information Distance and Entropy Reduction.
Villaverde AF, Ross J, Morán F, Banga JR.
PLoS One. 2014 May 7;9(5):e96732. doi: 10.1371/journal.pone.0096732. eCollection 2014.

MBMDR 4.4.1 – Model-Based Multifactor Dimensionality Reduction

MBMDR 4.4.1

:: DESCRIPTION

MBMDR (model-based multifactor dimensionality reduction) is a software that is able to detect multiple sets of significant gene-gene and/or gene-environment interactions in relation to a trait of interest, while efficiently controlling type I error rates. The trait can either be expressed on a binary scale, or on a continuous scale.

::DEVELOPER

the Statistical Genetics Research Club

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows with Cygwin

:: DOWNLOAD

 MBMDR

:: MORE INFORMATION

Citation

gammaMAXT: a fast multiple-testing correction algorithm.
Lishout FV, Gadaleta F, Moore JH, Wehenkel L, Steen KV.
BioData Min. 2015 Nov 20;8:36. doi: 10.1186/s13040-015-0069-x.

Bioinformatics. 2010 Sep 1;26(17):2198-9. Epub 2010 Jul 1.
mbmdr: an R package for exploring gene-gene interactions associated with binary or quantitative traits.
Calle ML, Urrea V, Malats N, Van Steen K.

MDR 3.0.2 – Multifactor Dimensionality Reduction

MDR 3.0.2

:: DESCRIPTION

MDR is a data mining strategy for detecting and characterizing nonlinear interactions among discrete attributes (e.g. SNPs, smoking, gender, etc.) that are predictive of a discrete outcome (e.g. case-control status). The MDR software combines attribute selection, attribute construction and classification with cross-validation to provide a powerful approach to modeling interactions.

::DEVELOPER

the Computational Genetics Laboratory in the Institute for Quantitative Biomedical Sciences at Dartmouth Medical Schooland Dartmouth College

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 MDR

:: MORE INFORMATION

Citation:

Ritchie, Hahn, Roodi, Bailey, Dupont, Parl, Moore (2001),
“Multifactorial dimensionality reduction reveals high-order interactions among estrogen metabolism genes in sporadic breat cancer“,
American Journal of Human Genetics, 69:138-147.

TRaCE 0.1 – Transitive Reduction and Closure Ensemble

TRaCE 0.1

:: DESCRIPTION

TRaCE is a new framework and algorithms for the ensemble inference of GRNs (gene regulatory networks).

:: DEVELOPER

Chemical and Biological Systems Engineering Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • MatLab

:: DOWNLOAD

 TRaCE

:: MORE INFORMATION

Citation

Ud-Dean, SMM., and Gunawan, R.
Ensemble Inference and Inferability of Gene Regulatory Networks.
PLoS ONE, 9(8), e103812 (2014)

FAM-MDR – Family-Based Multifactor Dimensionality Reduction

FAM-MDR

:: DESCRIPTION

FAM-MDR is a multifactor dimensionality reduction method for epistasis detection in small or extended pedigrees.

::DEVELOPER

the Statistical Genetics Research Club

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R package

:: DOWNLOAD

 FAM-MDR

:: MORE INFORMATION

Citation

FAM-MDR: a flexible family-based multifactor dimensionality reduction technique to detect epistasis using related individuals.
Cattaert T, Urrea V, Naj AC, De Lobel L, De Wit V, Fu M, Mahachie John JM, Shen H, Calle ML, Ritchie MD, Edwards TL, Van Steen K.
PLoS One. 2010 Apr 22;5(4):e10304.

GRAST 1.0 – Genome Reduction Analysing Software Tool

GRAST 1.0

:: DESCRIPTION

GRAST allows the user to analyse genome reduction by whole genome comparison between a reduced genome and a reference genome (a close relative to the reduced genome). A number of the options in GRAST can also be used for a whole genome comparison of non-reduced genomes.

::DEVELOPER

Dr Mario Fares 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl

:: DOWNLOAD

 GRAST

:: MORE INFORMATION

Citation

GRAST: a new way of genome reduction analysis using comparative genomics.
Toft C, Fares MA.
Bioinformatics. 2006 Jul 1;22(13):1551-61. Epub 2006 Apr 6.