Package: joda
Type: Package
Title: JODA algorithm for quantifying gene deregulation using knowledge
Version: 1.20.0
Date: 2011-04-03
Author: Ewa Szczurek
Description: Package 'joda' implements three steps of an algorithm
called JODA. The algorithm computes gene deregulation scores.
For each gene, its deregulation score reflects how strongly an
effect of a certain regulator's perturbation on this gene
differs between two different cell populations. The algorithm
utilizes regulator knockdown expression data as well as
knowledge about signaling pathways in which the regulators are
involved (formalized in a simple matrix model).
Reference: Szczurek E, Markowetz F, Gat-Viks I, Biecek P, Tiuryn J,
Vingron M: Deregulation upon DNA damage revealed by joint
analysis of context-specific perturbation data. Submitted.
Maintainer: Ewa Szczurek <szczurek@molgen.mpg.de>
Depends: R (>= 2.0), bgmm, RBGL
URL: http://www.bioconductor.org
License: GPL (>= 2)
biocViews: Microarray, Pathways, GraphAndNetwork, StatisticalMethod,
NetworkInference
NeedsCompilation: no
Packaged: 2016-05-04 03:57:45 UTC; biocbuild
Package: pkgDepTools
Type: Package
Title: Package Dependency Tools
Version: 1.38.0
Author: Seth Falcon
Maintainer: Seth Falcon <seth@userprimary.net>
Description: This package provides tools for computing and analyzing
dependency relationships among R packages. It provides tools
for building a graph-based representation of the dependencies
among all packages in a list of CRAN-style package
repositories. There are also utilities for computing
installation order of a given package. If the RCurl package is
available, an estimate of the download size required to install
a given package and its dependencies can be obtained.
License: GPL-2
Depends: methods, graph, RBGL
Imports: graph, RBGL
Suggests: Biobase, Rgraphviz, RCurl, BiocInstaller
LazyLoad: Yes
biocViews: Infrastructure, GraphAndNetwork
NeedsCompilation: no
Packaged: 2016-05-04 02:58:19 UTC; biocbuild
Package: CellNOptR
Type: Package
Title: Training of boolean logic models of signalling networks using
prior knowledge networks and perturbation data.
Version: 1.18.0
Date: 2014-03-13
Author: T.Cokelaer, F.Eduati, A.MacNamara, S.Schrier, C.Terfve
Maintainer: T.Cokelaer <cokelaer@ebi.ac.uk>
Depends: R (>= 2.15.0), RBGL, graph, methods, hash, ggplot2, RCurl, Rgraphviz, XML
Suggests: RUnit, BiocGenerics, igraph
biocViews: CellBasedAssays, CellBiology, Proteomics, TimeCourse
Description: This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.
License: GPL-3
LazyLoad: yes
SystemRequirements: Graphviz version >= 2.2
NeedsCompilation: yes
Packaged: 2016-05-04 04:18:04 UTC; biocbuild
Package: RpsiXML
Version: 2.14.0
Date: 2015-04-09
Title: R interface to PSI-MI 2.5 files
Author: Jitao David Zhang, Stefan Wiemann, Marc Carlson, with contributions from Tony Chiang
Maintainer: Jitao David Zhang <jitao_david.zhang@roche.com>
Depends: methods, annotate (>= 1.21.0), graph (>= 1.21.0), Biobase, RBGL (>= 1.17.0), XML (>= 2.4.0), hypergraph (>= 1.15.2), AnnotationDbi
Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db, hom.Hs.inp.db, hom.Mm.inp.db, hom.Dm.inp.db, hom.Rn.inp.db, hom.Sc.inp.db, Rgraphviz, ppiStats, ScISI
Description: Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously.
Collate: AllClasses.R AllGenerics.R AllMethods.R SAXhandlers.R
funcsAnnotation.R hyperGraphs.R psi25parser.R psimi25Source.R
validatePSIMI25.R graphSpeciesConverter.R
License: LGPL-3
URL: http://www.bioconductor.org
biocViews: Infrastructure, Proteomics
NeedsCompilation: no
Packaged: 2016-05-04 03:09:44 UTC; biocbuild
Package: BioNet
Type: Package
Title: Routines for the functional analysis of biological networks
Version: 1.32.0
Date: 2015-09-11
Author: Marcus Dittrich and Daniela Beisser
Maintainer: Marcus Dittrich
<marcus.dittrich@biozentrum.uni-wuerzburg.de>
Description: This package provides functions for the integrated
analysis of protein-protein interaction networks and the
detection of functional modules. Different datasets can be
integrated into the network by assigning p-values of
statistical tests to the nodes of the network. E.g. p-values
obtained from the differential expression of the genes from an
Affymetrix array are assigned to the nodes of the network. By
fitting a beta-uniform mixture model and calculating scores
from the p-values, overall scores of network regions can be
calculated and an integer linear programming algorithm
identifies the maximum scoring subnetwork.
License: GPL (>= 2)
Depends: R (>= 2.10.0), graph, RBGL
Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML
Imports: igraph (>= 1.0.1), AnnotationDbi, Biobase
LazyLoad: yes
URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/
biocViews: Microarray, DataImport, GraphAndNetwork, Network,
NetworkEnrichment, GeneExpression, DifferentialExpression
NeedsCompilation: no
Packaged: 2016-05-04 03:41:51 UTC; biocbuild
providing 
.