Package: tRanslatome
Type: Package
Title: Comparison between multiple levels of gene expression
Version: 1.10.0
Date: 2015-08-20
Author: Toma Tebaldi, Erik Dassi, Galena Kostoska
Maintainer: Toma Tebaldi <tebaldi@science.unitn.it>, Erik Dassi <erik.dassi@unitn.it>
Depends: R (>= 2.15.0), methods, limma, sigPathway, samr, anota, DESeq, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix, Biobase
Description: Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions (treated vs. untreated, diseased vs. normal, mutant vs. wild-type) among different levels of gene expression (transcriptome ,translatome, proteome), using several statistical methods: Rank Product, Translational Efficiency, t-test, SAM, Limma, ANOTA, DESeq, edgeR. Possibility to plot the results with scatterplots, histograms, MA plots, standard deviation (SD) plots, coefficient of variation (CV) plots. Detection of significantly enriched post-transcriptional regulatory factors (RBPs, miRNAs, etc) and Gene Ontology terms in the lists of DEGs previously identified for the two expression levels. Comparison of GO terms enriched only in one of the levels or in both. Calculation of the semantic similarity score between the lists of enriched GO terms coming from the two expression levels. Visual examination and comparison of the enriched terms with heatmaps, radar plots and barplots.
License: GPL-3
LazyLoad: yes
biocViews: CellBiology, GeneRegulation, Regulation, GeneExpression,
DifferentialExpression, Microarray, HighThroughputSequencing,
QualityControl, GO, MultipleComparisons, Bioinformatics
Packaged: 2016-05-04 04:58:42 UTC; biocbuild
NeedsCompilation: no
Package: phenoTest
Type: Package
Title: Tools to test association between gene expression and phenotype
in a way that is efficient, structured, fast and scalable. We
also provide tools to do GSEA (Gene set enrichment analysis)
and copy number variation.
Version: 1.20.0
Date: 2013-05-29
Author: Evarist Planet
Maintainer: Evarist Planet <evarist.planet@epfl.ch>
Description: Tools to test correlation between gene expression and
phenotype in a way that is efficient, structured, fast and
scalable. GSEA is also provided.
License: GPL (>=2)
Depends: R (>= 2.12.0), Biobase, methods, annotate, Heatplus, BMA, ggplot2
Imports: survival, limma, Hmisc, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, SNPchip, hgu133a.db, HTSanalyzeR, ellipse
Suggests: GSEABase, KEGG.db, GO.db
Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db,
org.Hs.eg.db, org.Dm.eg.db
LazyLoad: yes
biocViews: Microarray, DifferentialExpression, MultipleComparison,
Clustering, Classification
NeedsCompilation: no
Packaged: 2016-05-04 03:54:59 UTC; biocbuild
Package: GeneAnswers
Type: Package
Title: Integrated Interpretation of Genes
Version: 2.14.0
Date: 2014-10-1
Depends: R (>= 3.0.0), igraph, RCurl, annotate, Biobase (>= 1.12.0), methods, XML, RSQLite, MASS, Heatplus, RColorBrewer
Imports: RBGL, annotate, downloader
Suggests: GO.db, KEGG.db, reactome.db, biomaRt, AnnotationDbi, org.Hs.eg.db, org.Rn.eg.db, org.Mm.eg.db, org.Dm.eg.db, graph
Author: Lei Huang, Gang Feng, Pan Du, Tian Xia, Xishu Wang, Jing, Wen, Warren Kibbe and Simon Lin
Maintainer: Lei Huang <lhuang7@uchicago.edu> and Gang Feng <gilbertfeng@gmail.com>
Description: GeneAnswers provides an integrated tool for biological or medical interpretation of the given one or more groups of genes by means of statistical test.
License: LGPL (>= 2)
biocViews: Infrastructure, DataRepresentation, Visualization,
GraphsAndNetworks
LazyLoad: yes
Packaged: 2016-05-04 03:22:43 UTC; biocbuild
NeedsCompilation: no
providing 
.