csbl.go is an R package
for computing semantic similarity between genes using Gene Ontology
annotation and for clustering genes based on the similarity measures.
The package has been tested with R 2.8-3.0 on Windows and Linux.
csbl.go is licensed under
GNU General
Public License.
See the associated publication: Kristian Ovaska, Marko Laakso, Sampsa Hautaniemi. Fast Gene Ontology based clustering for microarray experiments. BioData Mining 2008, 1:11.
| File | Date | Download | Comments |
|---|---|---|---|
| User Guide | 2012-07-17 | userguide.pdf | Up-to-date with latest code. |
csbl.go 1.4.1 |
2013-10-07 |
Windows: R 3.0+ Windows: R 2.12+ Windows: R 2.x-2.11 Unix: Source |
Updated for latest GO (2013-09) and R 3.0. |
csbl.go 1.4.0 |
2012-07-17 |
Windows: R 2.12+ Windows: R 2.x-2.11 Unix: Source |
Updated for latest GO (2012-07). New organisms supported: Arabidopsis thaliana and Xenopus tropicalis. Added a code example to User Guide (heat map visualization). |
csbl.go 1.3.7 |
2011-12-19 |
Windows: R 2.12+ Windows: R 2.x-2.11 Unix: Source |
Updated for latest GO (2011-11) and R 2.14. |
csbl.go 1.3.6 |
2011-06-16 |
Windows: R 2.12+ Windows: R 2.x-2.11 Unix: Source |
Updated for latest GO (2011-06). |
csbl.go 1.3.5 |
2010-11-30 |
Windows: R 2.12+ Windows: R 2.x-2.11 Unix: Source |
Updated for latest GO (2010-11). |
csbl.go 1.3.4 |
2010-04-19 |
Windows: R 2.x-2.11 Unix: Source |
Fixed a bug in GO enrichment analysis that produced over-conservative p-values in Fisher's Exact Test; new p-values are smaller than previous p-values. Updated for latest GO (2010-04). |
csbl.go 1.3.3 |
2009-11-11 |
Windows: R 2.x-2.11 Unix: Source |
Updated for latest GO (2009-11). Fixed a crash in function ids.to.ontologies that occurs in some R versions. |
csbl.go 1.3.2 |
2009-05-30 |
Windows: R 2.x-2.11 Unix: Source |
Updated for latest GO (2009-05). |
csbl.go 1.3.1 |
2009-02-09 | Unix: Source | Windows users should download version 1.3 (below) as 1.3.1 only contains a fix for the Linux version. |
csbl.go 1.3 |
2008-11-17 |
Windows: R 2.x-2.11 Unix: Source |
Manuscript version. |
On Windows, download the Windows binary and install it from the R GUI
(Packages -> Install package(s) from local zips files).
On Unix, download the source package and install it using
R CMD INSTALL.
You also need to install some Bioconductor packages (Biobase, annotate, GO.db) and CRAN packages (cluster and RUnit).
Copyright 2007-2013 Kristian Ovaska, Marko Laakso.
TUT (C++ Template Unit Test Framework) Copyright 2002-2006 Vladimir Dyuzhev,
2007 Denis Kononenko.
Last updated: 2013-10-08