Diametrical Clustering – Identify Anti-correlated Gene Clusters

Diametrical Clustering

:: DESCRIPTION

Diametrical clustering is a software that explicitly identifies anti-correlated clusters of genes. Our algorithm proceeds by iteratively (i) re-partitioning the genes and (ii) computing the dominant singular vector of each gene cluster; each singular vector serving as the prototype of a ‘diametric’ cluster. We empirically show the effectiveness of the algorithm in identifying diametrical or anti-correlated clusters. Testing the algorithm on yeast cell cycle data, fibroblast gene expression data, and DNA microarray data from yeast mutants reveals that opposed cellular pathways can be discovered with this method.

::DEVELOPER

Usman Roshan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Diametrical Clustering

:: MORE INFORMATION

Citation

I. S. Dhillon, E. M. Marcotte, U. Roshan,
Diametrical Clustering for identifying anti- correlated gene clusters“,
Bioinformatics, 19, pp 1612-1619, 2003

KegArray 1.2.4 – Microarray Data Analysis & Cluster

KegArray 1.2.4

:: DESCRIPTION

KegArray is a Java application that provides an environment for analyzing both transcriptome data (gene expression profiles) and metabolome data (compound profiles). Tightly integrated with the KEGG database, KegArray enables you to easily map those data to KEGG resources including PATHWAY, BRITE and genome maps.

::DEVELOPER

Kanehisa Laboratories

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

KegArray

:: MORE INFORMATION

Citation

Methods Mol Biol. 2012;802:19-39.
The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals.
Kotera M, Hirakawa M, Tokimatsu T, Goto S, Kanehisa M.

VISDA 1.0 – Visualization, and Discovery for Cluster Analysis of Genomic data

VISDA 1.0

:: DESCRIPTION

VISDA (VIsual and Statistical Data Analyzer) is a software for cluster modeling, visualization, and discovery in genomic data. VISDA performs progressive, coarse-to-fine (divisive) hierarchical clustering and visualization, supported by hierarchical mixture modeling, supervised/unsupervised informative gene selection, supervised/unsupervised data visualization, and user/prior knowledge guidance, to discover hidden clusters within complex, high-dimensional genomic data.

::DEVELOPER

Computational Bioinformatics & Bio-imaging Laboratory (CBIL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 VISDA

:: MORE INFORMATION

Citation:

caBIG VISDA: modeling, visualization, and discovery for cluster analysis of genomic data.
Zhu Y, Li H, Miller DJ, Wang Z, Xuan J, Clarke R, Hoffman EP, Wang Y.
BMC Bioinformatics. 2008 Sep 18;9:383.

Genesis 1.8.1 / GenesisServer 1.1.0 – Cluster Analysis of Microarray data

Genesis 1.7.7 / GenesisServer 1.1.0

:: DESCRIPTION

Genesis integrates various tools for microarray data analysis such as filters, normalization and visualization tools, distance measures as well as common clustering algorithms including hierarchical clustering, self-organizing maps, k-means, principal component analysis, and support vector machines.

Genesis Server is an application server for computation of Hierarchical Clustering, Self Organizing Maps (SOM), k-means Clustering and Support Vector Machines (SVM).

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 Genesis , GenesisServer

:: MORE INFORMATION

Citation

Sturn A, Quackenbush J, Trajanoski Z.
Genesis: Cluster analysis of microarray data.
Bioinformatics. 2002 Jan;18(1):207-8.

Sturn A, Mlecnik B, Pieler R, Rainer J, Truskaller T, Trajanoski Z.
Client-Server environment for high-performance gene expression data analysis.
Bioinformatics. 19: 772-773 (2003)

MSClust 20130708 – Clustering 16S rRNA sequences into OTUs

MSClust 20130708

:: DESCRIPTION

MSClust (Multi-Seeds Based Clustering Algorithm) is an Matlab package for Clustering 16S rRNA sequences into OTUs.

::DEVELOPER

Zhao Hongyu’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Matlab

:: DOWNLOAD

 MSClust

:: MORE INFORMATION

Citation

J Microbiol Methods. 2013 Sep;94(3):347-55. doi: 10.1016/j.mimet.2013.07.004. Epub 2013 Jul 28.
MSClust: A Multi-Seeds based Clustering algorithm for microbiome profiling using 16S rRNA sequence.
Chen W1, Cheng Y, Zhang C, Zhang S, Zhao H.

ClusterA 1004 – Calculating Silhouette scores for Assessment of SNP Genotype Clusters

ClusterA 1004

:: DESCRIPTION

ClusterA is a tool for calculating some statistics on clusters, the most important being the “Silhouette Score” used in our group for genotype cluster validation.

::DEVELOPER

Molecular Medicine research group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ClusterA

:: MORE INFORMATION

Citation

Lovmar L, Ahlford A, Jonsson M, Syvänen A-C (2005)
Silhouette scores for assessment of SNP genotype clusters.
BMC Genomics 6:35

Kolmogorov – Compression-based Classification of Biological Sequences and Structures

Kolmogorov

:: DESCRIPTION

Kolmogorov is a multistep approach to classify and cluster Biological Sequences and Structures, via Compression.

::DEVELOPER

Raffaele Giancarlo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOSX / Windows
  • Perl
  • BioPerl

:: DOWNLOAD

 Kolmogorov

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Jul 13;8:252.
Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.
Ferragina P1, Giancarlo R, Greco V, Manzini G, Valiente G.

GenClust 2.0 – Clustering Gene Expression data

GenClust 2.0

:: DESCRIPTION

GenClust is a new genetic algorithm for clustering gene expression data. It has two key features: (a) a novel coding of the search space that is simple, compact and easy to update; (b) it can be used naturally in conjunction with data driven internal validation methods.

::DEVELOPER

Lo Bosco Giosuè , Raffaele Giancarlo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOSX / Windows

:: DOWNLOAD

 GenClust

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2005 Dec 7;6:289.
GenClust: a genetic algorithm for clustering gene expression data.
Di Gesú V1, Giancarlo R, Lo Bosco G, Raimondi A, Scaturro D.

ValWorkBench 1.0 – Java library for Cluster Validation

ValWorkBench 1.0

:: DESCRIPTION

ValWorkBench consists of a collection of measures for validation of clustering solutions and algorithms. It has external measures, as the Adjusted Rand index, and internal measures as Figure of Merit, Gap Statistics, Within Cluster Sum Square, Consensus Clustering and more.

::DEVELOPER

Raffaele Giancarlo

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOSX / Windows
  • Java

:: DOWNLOAD

 ValWorkBench

:: MORE INFORMATION

Citation

ValWorkBench: an open source Java library for cluster validation, with applications to microarray data analysis.
Giancarlo R, Scaturro D, Utro F.
Comput Methods Programs Biomed. 2015 Feb;118(2):207-17. doi: 10.1016/j.cmpb.2014.12.004.

HHCompare – HMM based protein Hierarchical Clustering

HHCompare

:: DESCRIPTION

HHCompare is a pipeline for HMM-HMM comparison based hierarchial clustering and analysis of potential paralogues in sequence set.

::DEVELOPER

Ranko Gacesa, King’s College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 HHCompare

:: MORE INFORMATION

Citation

Gene duplications are extensive and contribute significantly to the toxic proteome of nematocysts isolated from Acropora digitifera (Cnidaria: Anthozoa: Scleractinia).
Gacesa R, Chung R, Dunn SR, Weston AJ, Jaimes-Becerra A, Marques AC, Morandini AC, Hranueli D, Starcevic A, Ward M, Long PF.
BMC Genomics. 2015 Oct 13;16(1):774. doi: 10.1186/s12864-015-1976-4.