Recommend Easy To Use Microarray Clustering Software
9
7
Entering edit mode
14.4 years ago

Feel free to post your favorite clustering tool.

microarray clustering • 11k views
ADD COMMENT
11
Entering edit mode
14.4 years ago

One of my favorites is the MEV micro-array data analysis tool. It is simple to use and it has a very large number of features.

Works well for any type of data. You can also load into it data from a file that is in a simple text format:

GENE1, value1, value2
GENE2, value1, value2

Feel free to post your favorite clustering tool.

ADD COMMENT
1
Entering edit mode

It used to be a Java application that ran without problems as long as Java was properly installed. Did the requirements change in the meantime?

ADD REPLY
0
Entering edit mode

I just found that MEV was far from easy to install under linux.

ADD REPLY
10
Entering edit mode
13.9 years ago
Stew ★ 1.4k

My favourite clustering software is R. Some people may disagree about the 'easy to use' part but once you get over the initial slope of the learning curve it is very easy and hugely powerful. No other tool can really compare in my opinion. However if R is not for you then Cluster 3.0 and MapleTree are the way forward.

ADD COMMENT
2
Entering edit mode

@Eric: Clustering algorithms in R are quite many. Try for example: example(kmeans).

ADD REPLY
0
Entering edit mode

@Stew How is R a clustering software? What package or function do you use for clustering? Could you put a short example code here? Many thanks!

ADD REPLY
9
Entering edit mode
14.0 years ago

I am currently using Cluster 3.0 for clustering and TreeView.

ADD COMMENT
7
Entering edit mode
14.4 years ago
Zhenhai Zhang ▴ 170

I would recommend a combination of cluster and treeview.

pretty powerful!

ADD COMMENT
6
Entering edit mode
14.0 years ago
Alex ▴ 190

Possibly related: http://mmc.gnets.ncsu.edu/

ADD COMMENT
5
Entering edit mode
14.0 years ago
Geoffjentry ▴ 320

One thing you might look at is the Broad Institute's genepattern software. It can be clunky at times but it will do most common tasks in a fairly straightforward fashion.

ADD COMMENT
0
Entering edit mode

This would be my first choice as well.

ADD REPLY
2
Entering edit mode
13.4 years ago
Rm 8.3k

I use TM4 MultiExperiment Viewer (MeV), SMD and Eisen's Cluster3 with treeview. MeV has more capabilities to handle the microarray data.

Microarray Resources : Software and Tools

ADD COMMENT
1
Entering edit mode
13.4 years ago
Puthier ▴ 250

You may also try EXPANDER and SEURAT

ADD COMMENT
0
Entering edit mode
11.9 years ago

One thing you might look at is the Broad Institute's genepattern software. It can be clunky at times but it will do most common tasks in a fairly straightforward fashion herve leger

ADD COMMENT

Login before adding your answer.

Traffic: 2418 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6