Tag: Cluster

CRC 1.1 – Dirichlet Process Model-based Cluster

CRC 1.1

:: DESCRIPTION

CRC (Chinese Restaurant Cluster) implements a model-based Bayesian clustering algorithm. The cluster assignment procedure can be regarded as following a iterative Chinese restaurant process. This program is designed to cluster microarray gene expression data collected from multiple experiments. missing data is allowed. The program is written in C++, and can be run under Linux, Unix, Windows, MAC OSX operating system as a command line exexutable. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. Here is some more details on why you should try CRC for your microarray data analysis.

CRC Online Version

::DEVELOPER

Steve Qin @ the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX

:: DOWNLOAD

 CRC

:: MORE INFORMATION

Citation

Qin ZS.
Clustering microarray gene expression data using weighted Chinese restaurant process.
Bioinformatics. 2006 Aug 15;22(16):1988-97. Epub 2006 Jun 9.

CLOBB 2.0 – Cluster Sequences on the Basis of BLAST

CLOBB 2.0

:: DESCRIPTION

CLOBB (Cluster on the basis of BLAST similarity) takes a set of DNA sequences and clusters them into groups which putatively derive from the same gene. In order to operate, the user must have BLASTALL in their path. The output is a blastable fasta file named <cluster_id>EST, where cluster_id is given by the user, which contails a list of sequences with identifiers <cluster_id>00001 to <cluster_id>99999.

::DEVELOPER

John Parkinson (john.parkinson@ed.ac.uk) and Mark Blaxter , Institute of Cell, Animal and Population Biology, University of Edinburgh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

CLOBB

:: MORE INFORMATION

Citation:

John Parkinson , David B Guiliano and Mark Blaxter
Making sense of EST sequences by CLOBBing them
BMC Bioinformatics 2002, 3:31

Cluster 1.3 – Build Collections of Interacting Items

Cluster 1.3

:: DESCRIPTION

Cluster is a simple unix C++ program that builds collections of interacting items from records containing interacting pairs or larger fragments. It is part of the algorithm used in Reduce to find H-bond “cliques”

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux/ MacOsX/SGI-irix/Sun-SPARC

:: DOWNLOAD

Cluster

:: MORE INFORMATION

Cluster is free software available under the terms of its own BSD-style license.

MAGIC Tool 2.1 – MicroArray Genome Imaging & Clustering Tool

MAGIC Tool 2.1

:: DESCRIPTION

MAGIC Tool is an integrated microarray data analysis software.

The purpose of MAGIC Tool is to allow the user to begin with DNA microarray tiff files and end with biologically meaningful information. Comparative hybridization data (glass chips) and Affymetrix data are compatible with MAGIC Tool. You can start with tiff files or expression files.

MAGIC Tool allows the user to change parameters for clustering, data quantification etc.

::DEVELOPER

Laurie Heyer

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Mac/ Linux/ UNIX
  • Java

:: DOWNLOAD

MAGIC Tool ;  User’s Guide

:: MORE INFORMATION

Free software with open source.

Paper: MAGIC Tool: Integrated microarray data analysis (Bioinformatics, 2005)

Samster 2.0 – SAM to Cluster

Samster 2.0

:: DESCRIPTION

After doing a SAM analysis, you will want a more visual representation, or want to see if there is even more detailed substructure within these genes by using Cluster. Samster will take an Excel spreadsheet or text files and extract the raw data into a text output file, which can be fed directly into Cluster or opened in Treeview. Samster circumvents the need to create databases each time you wish to accomplish this task.

::DEVELOPER

Falkow Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac Os / Linux
  • Excel
  • Perl
  • TK

:: DOWNLOAD

Samster for Win ; Source Code ; Manual ; Sample input file

:: MORE INFORMATION

The software is copyrighted under the terms of the GNU General Public License. You can view this license at http://www.gnu.org/licenses/gpl.txt.

If you use SAMster, please cite:
Mueller A, O’Rourke J, Chu P, Kim CC, Sutton P, Lee A, Falkow S.
Protective immunity against Helicobacter is characterized by a unique transcriptional signature.
Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12289-94.