Question

Recommend Easy To Use Microarray Clustering Software

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15.2 years ago

Istvan Albert 102k

Feel free to post your favorite clustering tool.

microarray clustering • 11k views

ADD COMMENT • link updated 13 months ago by Ram 44k • written 15.2 years ago by Istvan Albert 102k

Ram · Answer 1 · 2009-10-05

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15.2 years ago

Istvan Albert 102k

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 • link updated 5.3 years ago by Ram 44k • written 15.2 years ago by Istvan Albert 102k

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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 • link 14.5 years ago by Istvan Albert 102k

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

ADD REPLY • link 14.5 years ago by Eric Normandeau 11k

Ram · Answer 2 · 2010-04-12

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14.6 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 • link updated 5.3 years ago by Ram 44k • written 14.6 years ago by Stew ★ 1.4k

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

ADD REPLY • link 14.2 years ago by Laurent Gautier ▴ 810

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@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 • link 14.5 years ago by Eric Normandeau 11k

Ram · Answer 3 · 2010-03-05

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14.7 years ago

Khader Shameer 18k

I am currently using Cluster 3.0 for clustering and TreeView.

ADD COMMENT • link updated 5.3 years ago by Ram 44k • written 14.7 years ago by Khader Shameer 18k

score 7 · Answer 4 · 2009-10-16

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15.1 years ago

Zhenhai Zhang ▴ 170

I would recommend a combination of cluster and treeview.

pretty powerful!

ADD COMMENT • link 15.1 years ago by Zhenhai Zhang ▴ 170

score 6 · Answer 5 · 2010-03-01

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14.8 years ago

Alex ▴ 190

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

ADD COMMENT • link 14.8 years ago by Alex ▴ 190

score 5 · Answer 6 · 2010-03-04

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14.7 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 • link 14.7 years ago by Geoffjentry ▴ 320

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This would be my first choice as well.

ADD REPLY • link 13.7 years ago by Larry_Parnell 16k

score 2 · Answer 7 · 2010-09-24

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14.2 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 • link 14.2 years ago by Rm 8.3k

score 1 · Answer 8 · 2010-09-23

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14.2 years ago

Puthier ▴ 250

You may also try EXPANDER and SEURAT

ADD COMMENT • link 13.6 years ago by Puthier ▴ 250

score 0 · Answer 9 · 2012-03-19

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12.7 years ago

Herve Leger • 0

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 • link 12.7 years ago by Herve Leger • 0