Package: ESEA
Version: 1.0
Title: ESEA: Discovering the Dysregulated Pathways based on Edge Set
Enrichment Analysis
Author: Junwei Han, Xinrui Shi, Chunquan Li
Maintainer: Xinrui Shi <xinrui103@163.com>
Description: The package can identify the dysregulated canonical pathways by investigating the changes of biological relationships of pathways in the context of gene expression data. (1) The ESEA package constructs a background set of edges by extracting pathway structure (e.g. interaction, regulation, modification, and binding etc.) from the seven public databases (KEGG; Reactome; Biocarta; NCI; SPIKE; HumanCyc; Panther) and the edge sets of pathways for each of the above databases. (2) The ESEA package can can quantify the change of correlation between genes for each edge based on gene expression data with cases and controls. (3) The ESEA package uses the weighted Kolmogorov-Smirnov statistic to calculate an edge enrichment score (EES), which reflects the degree to which a given pathway is associated the specific phenotype. (4) The ESEA package can provide the visualization of the results.
Depends: R (>= 2.10), igraph, XML, parmigene
Suggests: Matrix, graph
Collate: calEdgeCorScore.R ESEA.Main.R PlotGlobEdgeCorProfile.R
PlotPathwayGraph.R PlotRunEnrichment.R SavePathway2File.R
getEnvironmentData.R GetExampleData.R GetEdgesBackgrandData.R
GetPathwayEdgeData.R
LazyData: Yes
License: GPL (>= 2)
biocViews: Statistics, Pathways, edge, enrichment analysis
Packaged: 2015-01-22 12:50:32 UTC; Administrator
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-22 15:58:44
Package: synRNASeqNet
Type: Package
Title: Synthetic RNA-Seq Network Generation and Mutual Information
Estimates
Version: 1.0
Date: 2015-04-07
Author: Luciano Garofano, Stefano Maria Pagnotta, Michele Ceccarelli
Maintainer: Luciano Garofano <lucianogarofano88@gmail.com>
Depends: R (>= 3.1.1), parallel, parmigene, GenKern, igraph
URL: https://github.com/lucgar/synRNASeqNet
Imports: KernSmooth
Description: It implements various estimators of mutual information, such as
the maximum likelihood and the Millow-Madow estimator, various Bayesian
estimators, the shrinkage estimator, and the Chao-Shen estimator. It also
offers wrappers to the kNN and kernel density estimators. Furthermore, it
provides various index of performance evaluation such as precision, recall,
FPR, F-Score, ROC-PR Curves and so on. Lastly, it provides a brand new way
of generating synthetic RNA-Seq Network with known dependence structure.
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2015-04-20 08:45:39 UTC; luciano
Repository: CRAN
Date/Publication: 2015-04-20 11:55:18
Package: rsgcc
Type: Package
Title: Gini methodology-based correlation and clustering analysis of
microarray and RNA-Seq gene expression data
Version: 1.0.6
Author: Chuang Ma, Xiangfeng Wang
Maintainer: Chuang Ma <chuangma2006@gmail.com>
URL: http://www.cmbb.arizona.edu/
Depends: R (>= 2.15.1), biwt, cairoDevice, fBasics, grDevices, gplots, gWidgets, gWidgetsRGtk2, minerva, parmigene, stringr, snowfall
Suggests: bigmemory, ctc
Description: This package provides functions for calculating
associations between two genes with five correlation
methods(e.g., the Gini correlation coefficient [GCC], the
Pearson's product moment correlation coefficient [PCC], the
Kendall tau rank correlation coefficient [KCC], the Spearman's
rank correlation coefficient [SCC] and the Tukey's biweight
correlation coefficient [BiWt], and three non-correlation
methods (e.g., mutual information [MI] and the maximal
information-based nonparametric exploration [MINE], and the
euclidean distance [ED]). It can also been implemented to
perform the correlation and clustering analysis of
transcriptomic data profiled by microarray and RNA-Seq
technologies. Additionally, this package can be further applied
to construct gene co-expression networks (GCNs).
LazyLoad: yes
License: GPL (>= 2)
Date: 2013-06-12
Packaged: 2013-06-18 01:18:38 UTC; wanglab
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-06-18 07:40:43
providing 
.