[BiO BB] gene expression software for mere biologists?
veredcc at bgu.ac.il
Tue Dec 23 02:39:25 EST 2008
I highly recommend Partek, Spotfire (both commercial), Expander (mainly
clustering and functional analysis) and GSEA (functional analysis)
Vered Caspi, Ph.D.
Bioinformatics Core Facility, Head
National Institute for Biotechnology in the Negev
Building 39, room 214
Ben-Gurion University of the Negev
Beer-Sheva 84105, Israel
Email: veredcc at bgu.ac.il
Tel: 08-6479034 054-7915969
From: bbb-bounces at bioinformatics.org [mailto:bbb-bounces at bioinformatics.org]
On Behalf Of Harry Mangalam
Sent: Monday, December 22, 2008 8:40 PM
Subject: [BiO BB] gene expression software for mere biologists?
This may be a difficult query for this group to answer as the
readership is canted heavily in the geek direction, but what gene
expression software are you and your users relying on for gene
expression and pathway analysis?
I tilt heavily towards R/Bioconductor and other free software, so I'm
aware of the advantages of it, but we have non-commandline tool
researchers who are in need of tools they can use to examine the
results of gene expression studies.
This is something of a no-win - those tools that are very easy to use
tend to hide the very complexity that the user has to address, and so
the 'ease of use' / 'ease of thought' tends to weaken an already iffy
That said, are there tools (commercial or free) that provide fairly
good tradeoffs between power and ease of use for a non-geek biologist
user. ie runs on Mac & Windows and is mostly GUI? (If you have
experience in introducing such users to R, I'd also be interested in
Due to some aggressive pushing from the local SAS consulting group, we
are in the startup phase of a campus-wide, 1 year trial of
JMP/Genomics. JMP is a fairly cheap, nicely designed, multiplatform
GUI stats package from SAS. The Genomics part tho is an expensive
add-on that runs only on Windows and depends on an optional, even
more expensive Pathways package from InGenuity. The local research
community does not have a problem paying for such software if it
truly does work easily and well. If you have used it and have an
opinion or evaluation, I'd love to hear from you via email or phone.
Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway,
UC Irvine 92697 949 824-0084(o), 949 285-4487(c)
Good judgment comes from experience;
Experience comes from bad judgment. [F. Brooks.]
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