Tag: Clustering

iCluster 2.1.0 / iClusterPlus 0.99.4 – Integrative Clustering of Multiple Genomic Data Types

iCluster 2.1.0 / iClusterPlus 0.99.4

:: DESCRIPTION

iCluster is a softwaer of integrative clustering of multiple genomic data types using a joint latent variable model.

iClusterPlus is a software for pattern discovery and cancer gene identification in integrated cancer genomic data

::DEVELOPER

Ronglai Shen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • R package

:: DOWNLOAD

 iCluster / iClusterPlus

:: MORE INFORMATION

Citation:

Bioinformatics. 2009 Nov 15;25(22):2906-12. doi: 10.1093/bioinformatics/btp543.
Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis.
Shen R, Olshen AB, Ladanyi M.

Proc Natl Acad Sci U S A. 2013 Mar 12;110(11):4245-50. doi: 10.1073/pnas.1208949110.
Pattern discovery and cancer gene identification in integrated cancer genomic data.
Mo Q, Wang S, Seshan VE, Olshen AB, Schultz N, Sander C, Powers RS, Ladanyi M, Shen R.

GWproxy – Clustering Metagenome Short Reads using Weighted Proteins

GWproxy

:: DESCRIPTION

GWproxy is a software for clustering metagenome short reads. The software incorporates biological knowledge in the clustering process, by means of a list of proteins associated to
each read. These proteins are chosen from a reference proteome database according to their similarity with the given read, as evaluated by BLAST.

::DEVELOPER

Fabio Gori

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GWproxy

:: MORE INFORMATION

Citation

Gianluigi Folino, Fabio Gori, Mike S. M. Jetten, and Elena Marchiori.
Clustering metagenome short reads using weighted proteins.
In Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, 7th European Conference, EvoBIO 2009, Tübingen, Germany, April 15-17, 2009, Proceedings, volume 5483 of Lecture Notes in Computer Science, pages 152-163. Springer, 2009.

CLEAN 1.3.1 – CLustering Enrichment ANalysis

CLEAN  1.3.1

:: DESCRIPTION

 CLEAN is a computational framework for analytically and visually integrating knowledge-based functional categories with the cluster analysis of genomics data. The framework is based on the simple, conceptually appealing, and biologically interpretable gene-specific functional coherence score (CLEAN score). The score is derived by correlating the clustering structure as a whole with functional categories of interest.

:: DEVELOPER

Laboratory for Statistical Genomics, Univ. Cincinnati

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • R Package

:: DOWNLOAD

 CLEAN

:: MORE INFORMATION

Citation:

Freudenberg JM, Joshi VK, Hu Z, Medvedovic M.
CLEAN: CLustering Enrichment ANalysis.
BMC Bioinformatics (2009) 10:234. Pubmed. Poster presented at OCCBIO 2008.

Excavator 2.0 – Gene Expression Data Clustering

Excavator 2.0

:: DESCRIPTION

Excavator (EXpression data Clustering Analysis and VisualizATiOn Resource) is a computer software program for gene expression data clustering. It uses a set of unique clustering algorithms developed by the Computational Systems Biology Lab (CSBL) at the University of Georgia. Excavator represents data internally as a minimum spanning tree and outputs results to the user through the use of a micro-array data window, graphs, and a dendrogram viewer.

::DEVELOPER

The Computational Systems Biology Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 Excavator

:: MORE INFORMATION

Citation

Dong Xu, Victor Olman, Li Wang and Ying Xu
Excavator: a computer program for efficiently mining gene expression data
Nucl. Acids Res. (2003) 31 (19): 5582-5589.

PuReD-MCL 20111130 – PubMed Document Clustering

PuReD-MCL 20111130

:: DESCRIPTION

PuReD-MCL (PUbmed RElated Document – MCL) is an efficient algorithm for PubMed document clustering (based on the MCL algorithm) using pre-computed document relatedness.

::DEVELOPER

The Bioinformatics Analysis Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 PuReD-MCL

:: MORE INFORMATION

Citation:

Bioinformatics. 2008 Sep 1;24(17):1935-41. Epub 2008 Jul 1.
PuReD-MCL: a graph-based PubMed document clustering methodology.
Theodosiou T, Darzentas N, Angelis L, Ouzounis CA.

Otupipe 1.1.9 – OTU Clustering pipeline for Next-gen reads

Otupipe 1.1.9

:: DESCRIPTION

The otupipe script creates OTUs from next-generation sequence reads for single-region experiments such as 16S and ITS. Otupipe performs error-correction, amplicon and abundance estimation, chimera detection (using UCHIME) and OTU clustering.

::DEVELOPER

Robert Edgar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 otupipe

:: MORE INFORMATION

RAMMCAP 20130510 – Rapid Analysis of Multiple Metagenomes with a Clustering and Annotation Pipeline

RAMMCAP 20130510

:: DESCRIPTION

RAMMCAP is a metagenomic analysis package developed using an ultra-fast sequence clustering algorithm, fast protein family annotation tools, and a novel statistical metagenome comparison method that employs a unique graphic interface. RAMMCAP processes extremely large datasets with only moderate computational effort.

::DEVELOPER

Group of Weizhong Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

  RAMMCAP

:: MORE INFORMATION

Citation

Weizhong Li.
Analysis and comparison of very large metagenomes with fast clustering and functional annotation.
BMC Bioinformatics 2009, 10:359 doi:10.1186/1471-2105-10-359

WCD 0.6.3 – DNA Sequence Clustering tool

WCD 0.6.3

:: DESCRIPTION

WCD (wcdest – Tool for clustering Expressed Sequence Tags (ESTs) ) is a DNA sequence clustering tool. It reads in a set of DNA sequences (typically ESTs or mRNAs) in FASTA format and organises them into clusters of similar sequences, producing a list of clusters and their members on standard output.

::DEVELOPER

Scott Hazelhurst and his team at the University of the Witwatersrand

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOSX

:: DOWNLOAD

 WCD

:: MORE INFORMATION

Citation:

An overview of the wcd EST clustering tool.
Hazelhurst S, Hide W, Lipták Z, Nogueira R, Starfield R.
Bioinformatics. 2008 Jul 1;24(13):1542-6.

Simcluster 0.9.2 – Clustering Enumeration Gene Expression data on the Simplex Space

Simcluster 0.9.2

:: DESCRIPTION

Simcluster is a package for clustering analysis of transcript enumeration data on the simplex space.

::DEVELOPER

Shmulevich Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Simcluster

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Jul 11;8:246.
Simcluster: clustering enumeration gene expression data on the simplex space.
Vêncio RZ, Varuzza L, de B Pereira CA, Brentani H, Shmulevich I.

JESAM 0.8.1 – Parallel Processing DNA Sequence Comparison and Clustering

JESAM 0.8.1

:: DESCRIPTION

JESAM is a software components to create and publish EST alignments and clusters.

::DEVELOPER

Jeremy Parsons

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  JESAM

:: MORE INFORMATION

Citation

Bioinformatics. 2000 Apr;16(4):313-25.
JESAM: CORBA software components to create and publish EST alignments and clusters.
Parsons JD, Rodriguez-Tomé P.

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