Package: mseapca
Type: Package
Title: Metabolite set enrichment analysis for factor loading in
principal component analysis
Version: 1.0
Date: 2012-04-10
Author: Hiroyuki Yamamoto
Maintainer: Hiroyuki Yamamoto <h.yama2396@gmail.com>
Description: This package provides functions for metabolite set
enrichment analysis (MSEA) and principal component analysis
(PCA), and converting metabolite set list from your own csv
files or KEGG's tar.gz files to XML documents. This package is
suitable for computation of MSEA for factor loading in PCA.
License: BSD
Depends: XML
Packaged: 2012-04-15 04:16:03 UTC; yamamoto
Repository: CRAN
Date/Publication: 2012-04-15 16:42:20
Package: MUCflights
Title: Munich Franz-Josef-Strauss Airport Pattern Analysis
Version: 0.0-3
Date: 2011-02-21
Author: The students of the `Advanced R Programming Course' Basil Abou
El-Komboz, Andreas Bender, Abdelilah El Hadad, Laura Goeres,
Roman Hornung, Max Hughes-Brandl, Christian Lindenlaub,
Christina Riedel, Ariane Straub, Florian Wickler under the
supervision of Manuel Eugster and Torsten Hothorn
Maintainer: Manuel Eugster <Manuel.Eugster@stat.uni-muenchen.de>
Description: Functions for downloading flight data from
http://www.munich-airport.de and for analyzing flight patterns.
License: GPL (>= 2)
Depends: XML, geosphere (>= 1.2-15), sp, RSQLite, NightDay
URL: http://www.youtube.com/watch?v=y3RW_N-TPb4
LazyLoad: yes
Packaged: 2011-02-22 08:00:21 UTC; hothorn
Repository: CRAN
Date/Publication: 2011-02-22 08:14:43
Package: EIAdata
Type: Package
Title: R Wrapper for the Energy Information Administration (EIA) API
Version: 0.0.3
Date: 2015-03-09
Author: Matthew Brigida
Maintainer: Matthew Brigida <matt@complete-markets.com>
Description: An R wrapper to allow the user to query categories and Series IDs, and import data, from the EIA's API.
Depends: R (>= 2.11.0), XML, plyr, xts, zoo
License: GPL-2
Packaged: 2015-03-10 03:32:56 UTC; matt
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-10 06:58:50
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: EcoHydRology
Version: 0.4.12
Title: A community modeling foundation for Eco-Hydrology.
Author: Fuka DR, Walter MT, Archibald JA, Steenhuis TS, and Easton ZM
Maintainer: Daniel Fuka <drf28@cornell.edu>
Depends: R (>= 2.10), operators, topmodel, DEoptim, XML
Description: This package provides a flexible foundation for scientists,
engineers, and policy makers to base teaching exercises as well as for
more applied use to model complex eco-hydrological interactions.
License: GPL-2
Repository: CRAN
Date/Publication: 2014-04-04 08:09:55
KeepSource: TRUE
Packaged: 2014-04-03 23:55:45 UTC; dan
NeedsCompilation: no
Package: EcoTroph
Type: Package
Title: EcoTroph R package
Version: 1.6
Date: 2013-08-31
Author: J. Guitton, M. Colleter, P. Gatti, and D. Gascuel
Maintainer: Jerome Guitton <jerome.guitton@agrocampus-ouest.fr>
URL: http://sirs.agrocampus-ouest.fr/EcoTroph/
Description: EcoTroph is an approach and software for modelling marine and freshwater ecosystems. It is articulated entirely around trophic levels. EcoTroph's key displays are bivariate plots, with trophic levels as the abscissa, and biomass flows or related quantities as ordinates. Thus, trophic ecosystem functioning can be modelled as a continuous flow of biomass surging up the food web, from lower to higher trophic levels, due to predation and ontogenic processes. Such an approach, wherein species as such disappear, may be viewed as the ultimate stage in the use of the trophic level metric for ecosystem modelling, providing a simplified but potentially useful caricature of ecosystem functioning and impacts of fishing. This version contains catch trophic spectrum analysis (CTSA) function and corrected versions of the mf.diagnosis and create.ETmain functions.
License: GPL
LazyLoad: yes
Depends: XML
Packaged: 2013-09-13 12:22:22 UTC; jerome
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-09-13 15:44:12
Package: ONETr
Type: Package
Title: Efficient Authenticated Interaction with the O*NET API
Version: 1.0.3
Date: 2015-08-23
Author: Eric Knudsen
Maintainer: Eric Knudsen <eknudsen@gc.cuny.edu>
Description: Provides a series of functions designed to enable users to easily search and interact with occupational data from the O*NET API <www.onetonline.org>. The package produces parsed and listed XML data for custom interactions, or pre-packaged functions for easy extraction of specific data (e.g., Knowledge, Skills, Abilities, Work Styles, etc.).
Depends: XML, RCurl, plyr
License: GPL-3
NeedsCompilation: no
Packaged: 2015-08-24 16:07:42 UTC; eknudsen
Repository: CRAN
Date/Publication: 2015-08-25 01:01:23
Package: StatDataML
Version: 1.0-26
Title: Read and Write StatDataML Files
Authors@R: c(person(given = "David", family = "Meyer", role = c("aut", "cre"), email = "David.Meyer@R-project.org"),
person(given = "Torsten", family = "Hothorn", role = c("aut")),
person(given = "Friedrich", family = "Leisch", role = "aut"))
Description: Support for reading and writing files in StatDataML---an XML-based data exchange format.
Depends: R (>= 2.0.0), XML, utils
License: GPL-2
NeedsCompilation: no
Packaged: 2015-07-07 16:43:07 UTC; david
Author: David Meyer [aut, cre],
Torsten Hothorn [aut],
Friedrich Leisch [aut]
Maintainer: David Meyer <David.Meyer@R-project.org>
Repository: CRAN
Date/Publication: 2015-07-08 17:11:01
Package: SubpathwayGMir
Type: Package
Title: Identify Metabolic Subpathways Mediated by MicroRNAs
Version: 1.0
Date: 2015-05-20
Author: Li Feng, Chunquan Li and Xia Li
Maintainer: Li Feng <biofengfeng@sina.com>
Description: Routines for identifying metabolic subpathways mediated by microRNAs (miRNAs) through topologically locating miRNAs and genes within reconstructed Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway graphs embedded by miRNAs. (1) This package can obtain the reconstructed KEGG metabolic pathway graphs with genes and miRNAs as nodes, through converting KEGG metabolic pathways to graphs with genes as nodes and compounds as edges, and then integrating miRNA-target interactions verified by low-throughput experiments from four databases (TarBase, miRecords, mirTarBase and miR2Disease) into converted pathway graphs. (2) This package can locate metabolic subpathways mediated by miRNAs by topologically analyzing the "lenient distance" of miRNAs and genes within reconstructed KEGG metabolic pathway graphs.(3) This package can identify significantly enriched miRNA-mediated metabolic subpathways based on located subpathways by hypergenomic test. (4) This package can support six species for metabolic subpathway identification, such as caenorhabditis elegans, drosophila melanogaster, danio rerio, homo sapiens, mus musculus and rattus norvegicus, and user only need to update interested organism-specific environment variables.
Depends: R (>= 3.0.2), XML, igraph
Collate: fdr.est.R getBackground.R getEdgeLabel.R getEdgeLty.R
getInteGraphList.R GetK2riData.R getLayout.R getLocSubGraph.R
getOneNodePath.R getSymbolFromGene.R identifyGraph.R
initializeK2ri.R plotGraph.R printGraph.R updateOrgEnvir.R
mytriangle.R
LazyData: Yes
License: GPL (>= 2)
biocViews: Statistics, Annotation, SubPathways, Graphs, MicroRNAs
Packaged: 2015-05-20 06:50:06 UTC; sunyao
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-20 14:15:38