Question: Recommend Easy To Use Microarray Clustering Software
7
gravatar for Istvan Albert
7.5 years ago by
Istvan Albert ♦♦ 70k
University Park, USA
Istvan Albert ♦♦ 70k wrote:

Feel free to post your favorite clustering tool.

microarray clustering • 7.3k views
ADD COMMENTlink modified 7.5 years ago by Herve Leger0 • written 7.5 years ago by Istvan Albert ♦♦ 70k
11
gravatar for Istvan Albert
7.5 years ago by
Istvan Albert ♦♦ 70k
University Park, USA
Istvan Albert ♦♦ 70k wrote:

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 COMMENTlink written 7.5 years ago by Istvan Albert ♦♦ 70k
1

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 REPLYlink written 6.8 years ago by Istvan Albert ♦♦ 70k

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

ADD REPLYlink written 6.8 years ago by Eric Normandeau9.2k
10
gravatar for Stew
7.0 years ago by
Stew1.3k
Cambridge
Stew1.3k wrote:

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 COMMENTlink written 7.0 years ago by Stew1.3k
2

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

ADD REPLYlink written 6.5 years ago by Laurent Gautier810

@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 REPLYlink written 6.8 years ago by Eric Normandeau9.2k
8
gravatar for Khader Shameer
7.1 years ago by
Manhattan, NY
Khader Shameer17k wrote:

I am currently using Cluster 3.0 for clustering and TreeView.

ADD COMMENTlink written 7.1 years ago by Khader Shameer17k
7
gravatar for Zhenhai Zhang
7.4 years ago by
Zhenhai Zhang160
502 Wartik Lab, Penn State Univ
Zhenhai Zhang160 wrote:

I would recommend a combination of cluster and treeview.

pretty powerful!

ADD COMMENTlink written 7.4 years ago by Zhenhai Zhang160
6
gravatar for Alex
7.1 years ago by
Alex190
Alex190 wrote:

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

ADD COMMENTlink written 7.1 years ago by Alex190
5
gravatar for Geoffjentry
7.1 years ago by
Geoffjentry310
MA
Geoffjentry310 wrote:

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 COMMENTlink written 7.1 years ago by Geoffjentry310

This would be my first choice as well.

ADD REPLYlink written 6.1 years ago by Larry_Parnell15k
2
gravatar for Rm
6.5 years ago by
Rm7.4k
Danville, PA
Rm7.4k wrote:

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 COMMENTlink written 6.5 years ago by Rm7.4k
1
gravatar for Puthier
6.5 years ago by
Puthier250
Puthier250 wrote:

You may also try EXPANDER and SEURAT

ADD COMMENTlink modified 6.0 years ago • written 6.5 years ago by Puthier250
0
gravatar for Herve Leger
5.0 years ago by
Herve Leger0 wrote:

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 COMMENTlink written 5.0 years ago by Herve Leger0
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