Array File Maker 4.0 - B.J.
Breitkreutz et al. (Samuel Lunenfeld Research Institute, Mount
Sinai
Hospital) have created a series of programs that manipulate and manage DNA
microarray data. Given a
database of expression ratios, AFM 4.0 generates input
files for clustering, helps prepare colored figures and
Venn diagrams, and can
uncover aneuploidy in yeast microarray data.
AMIADA is an integrated computer program for organizing, exploring, visualizing, and analyzing
microarray
data produced by X. Xia (University of Ottawa). It features an EXCEL-like user interface and performs
data transformation, principal component analysis, a variety of cluster analysis
and extensive graphic functions for visualizing expression profiles.
Cluster: Perform a variety of types of cluster analysis and other types of processing on
large microarray datasets. Currently includes hierarchical clustering, self-organizing maps
(SOMs), k-means
clustering, principal component analysis.Hierarchical clustering methods described in Eisen et al. (1998) PNAS
95:14863.
ScanAlyze [Download]: Process fluorescent images of microarrays. Includes semi-
automatic definition of grids and complex pixel and spot analyses. Outputs
to tab-delimited text files for transfer
to any database. Written by Michael Eisen.
OligoWiz
- provides intelligent design of oligonucleotides for DNA microarrays. See: Design of oligonucleotides
for microarrays and perspectives for design of multi-transcriptome arrays. Henrik Bjørn Nielsen, Rasmus
Wernersson and Steen Knudsen. Nucleic Acids Research, 2003,
31: 3491-3496.