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: RNAither
Title: Statistical analysis of high-throughput RNAi screens
Version: 2.20.0
Author: Nora Rieber and Lars Kaderali, University of Heidelberg,
Viroquant Research Group Modeling, Im Neuenheimer Feld 267,
69120 Heidelberg, Germany
Maintainer: Lars Kaderali <lars.kaderali@uni-greifswald.de>
Depends: R (>= 2.10), topGO, RankProd, prada
Imports: geneplotter, limma, biomaRt, car, splots, methods
Description: RNAither analyzes cell-based RNAi screens, and includes
quality assessment, customizable normalization and statistical
tests, leading to lists of significant genes and biological
processes.
License: Artistic-2.0
biocViews: CellBasedAssays, QualityControl, Preprocessing,
Visualization, Annotation, GO
NeedsCompilation: no
Packaged: 2016-05-05 01:59:59 UTC; biocbuild
Package: ccTutorial
Type: Package
Title: Data package for ChIP-chip tutorial
Version: 1.10.0
Date: 2009-09-14
Author: Joern Toedling, Wolfgang Huber
Maintainer: Joern Toedling <joern.toedling@curie.fr>
Depends: R (>= 2.10), Ringo (>= 1.9.8), affy (>= 1.23.4), topGO (>=
1.13.1)
Imports: Biobase
Suggests: biomaRt, Biobase (>= 2.5.5), xtable
Description: This is a data package that accompanies a ChIP-chip
tutorial, which has been published in PLoS Computational Biology.
The data and source code in this package allow the reader to
completely reproduce the steps in the tutorial.
References: Joern Toedling and Wolfgang Huber (2008) Analyzing
ChIP-chip Data Using Bioconductor. PLoS Computational Biology,
4(11):e1000227.
License: Artistic-2.0
biocViews: ExperimentData, Mus_musculus_Data, MicroarrayData,
ChipOnChipData
NeedsCompilation: no
Packaged: 2016-05-07 20:16:08 UTC; biocbuild
Package: cellTree
Title: Inference and visualisation of Single-Cell RNA-seq data as a
hierarchical tree structure
Version: 1.2.2
Authors@R: c(person("David", "duVerle", email = "dave@cb.k.u-tokyo.ac.jp", role = c("aut",
"cre")), person("Koji", "Tsuda", email = "tsuda@k.u-tokyo.ac.jp", role = c("aut")))
Authors: David duVerle [aut, cre], Koji Tsuda [aut]
Encoding: UTF-8
Description: This packages computes a Latent Dirichlet Allocation (LDA) model of single-cell
RNA-seq data and builds a compact tree modelling the relationship between
individual cells over time or space.
Depends: R (>= 3.3), topGO
License: Artistic-2.0
LazyData: true
RoxygenNote: 5.0.1
VignetteBuilder: knitr
URL: http://tsudalab.org
Imports: topicmodels, slam, maptpx, igraph, xtable, gplots
Suggests: BiocStyle, knitr, HSMMSingleCell, biomaRt, org.Hs.eg.db, Biobase, tools
biocViews: Sequencing, RNASeq, Clustering, GraphAndNetwork,
Visualization, GeneExpression, GeneSetEnrichment,
BiomedicalInformatics, CellBiology, FunctionalGenomics,
SystemsBiology, GO, TimeCourse, Microarray
NeedsCompilation: no
Author: David duVerle [aut, cre], Koji Tsuda [aut]
Maintainer: David duVerle <dave@cb.k.u-tokyo.ac.jp>
Packaged: 2016-05-16 05:56:07 UTC; biocbuild
providing 
.