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csbl.go specifications

Information


Unique identifier OMICS_10330
Name csbl.go
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.4.1
Stability Stable
Requirements
Biobase, annotate, GO.db, cluster, Runit
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Kristian Ovaska

Publications for csbl.go

csbl.go citations

 (8)
library_books

Deregulated expression of HDAC9 in B cells promotes development of lymphoproliferative disease and lymphoma in mice

2016
PMCID: 5200892
PMID: 27799148
DOI: 10.1242/dmm.023366

[…] ch Tool for the Retrieval of Interacting Genes/Proteins STRING v9.1 (http://string-db.org) to develop interactomes or networks () and the KEGG pathway database (). GO () clustering was performed with csbl.go (). Partek Genomics Suite 6.6 was additionally used for data set analysis and comparisons. […]

library_books

TopoICSim: a new semantic similarity measure based on gene ontology

2016
BMC Bioinformatics
PMCID: 4966780
PMID: 27473391
DOI: 10.1186/s12859-016-1160-0

[…] The R programming language (version 3.2.2) was used for developing and running all programs. We used all the EC codes as annotation terms. The ppiPre (version 1.9), GeneSemSim (version 1.28.2), and csbl.go (version 1.4.1) packages were used to calculate IntelliGO, Wang, and SimGIC measures [–]. The DC values were estimated using the energy (version 1.6.2) package []. The SOM algorithm was perfor […]

library_books

Insights from systems pharmacology into cardiovascular drug discovery and therapy

2014
BMC Syst Biol
PMCID: 4297424
PMID: 25539592
DOI: 10.1186/s12918-014-0141-z

[…] n (MF) branches of the Gene Ontology (GO) from the GO database []. GO-based semantic similarity scores (GSS) between cardiovascular targets and genes were calculated according to Resnik [], using the csbl.go R package [] selecting the option to use all three ontologies. We calculated the average GSS of all pairs of cardiovascular target and gene. Random controls were obtained by selecting the same […]

library_books

Functional Network Based Gene Set Analysis Using Gene Ontology

2013
PLoS One
PMCID: 3572115
PMID: 23418449
DOI: 10.1371/journal.pone.0055635

[…] ations when calculating the pair-wise gene-gene similarities.To construct the functional network for the various GOGANPA variants, we first obtain pairwise gene similarity matrix using the R package csbl.go , version 1.3.6, available from the package website. We only use GO Biological Process functional annotations for similarity calculation. To obtain the adjacency matrix , the power-law goodnes […]

library_books

The preservation of bidirectional promoter architecture in eukaryotes: what is the driving force?

2012
BMC Syst Biol
PMCID: 3403606
PMID: 23046569
DOI: 10.1186/1752-0509-6-S1-S21

[…] ulated in all three GO subsystems: "biological process", "molecular function", "cellular component", employing an R package for computing semantic similarity based on Gene Ontology annotations called csbl.go []. […]

library_books

Functional organization and its implication in evolution of the human protein protein interaction network

2012
BMC Genomics
PMCID: 3375200
PMID: 22530615
DOI: 10.1186/1471-2164-13-150

[…] ce was used because it considers the dependence of the annotation terms, which is reflected in the covariance matrix. We also used a two-step semantic similarity based method implemented by R package csbl.go []. In this method, the semantic similarity between each pair of GO annotation terms was first computed according to Resnik [] and gene functional similarity was then measured by the maximum o […]

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csbl.go institution(s)
Computational Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Program, Biomedicum Helsinki, University of Helsinki, university of helsinki, Finland

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