Platform Design Info for Affymetrix DroGene-1_1-st.

PartheenMetaData http://swegene.onk.lu.se Annotation Data (PartheenMetaData) assembled using data from public repositories.

Platform Design Info for The Manufacturer's Name Sugar_Cane.

Platform Design Info for NimbleGen hg18_60mer_expr.

Platform Design Info for Affymetrix CynGene-1_0-st.

Platform Design Info for The Manufacturer's Name Yeast_2.

This package performs tests for paired high-throughput data.

Platform Design Info for The Manufacturer's Name Rat230_2.

Platform Design Info for The Manufacturer's Name HG-U133B.

Platform Design Info for NimbleGen 081229_hg18_promoter_medip_hx1.

Platform Design Info for The Manufacturer's Name Medicago.

Account for missing values in label-free mass spectrometry data without imputation. The package implements a probabilistic dropout model that ensures that the information from observed and missing values are properly combined. It adds empirical Bayesian priors to increase power to detect differentially abundant proteins.

Platform Design Info for Affymetrix SoyGene-1_1-st.

Platform Design Info for NimbleGen charm_hg18_example.

This package provides a GUI interface for the DAPAR package. The package Prostar (Proteomics statistical analysis with R) is a Bioconductor distributed R package which provides all the necessary functions to analyze quantitative data from label-free proteomics experiments. Contrarily to most other similar R packages, it is endowed with rich and user-friendly graphical interfaces, so that no programming skill is required.

Platform Design Info for NimbleGen 2006-10-31_rn34_refseq_promoter.

Platform Design Info for The Manufacturer's Name Xenopus_laevis.

peakCombiner, a fully R based, user-friendly, transparent, and customizable tool that allows even novice R users to create a high-quality consensus peak list. The modularity of its functions allows an easy way to optimize input and output data. A broad range of accepted input data formats can be used to create a consensus peak set that can be exported to a file or used as the starting point for most downstream peak analyses.

Platform Design Info for The Manufacturer's Name Poplar.

Platform Design Info for The Manufacturer's Name Canine_2.

The package is an R wrapper for Progenetix REST API built upon the Beacon v2 protocol. Its purpose is to provide a seamless way for retrieving genomic data from Progenetix database—an open resource dedicated to curated oncogenomic profiles. Empowered by this package, users can effortlessly access and visualize data from Progenetix.

The phenomis package provides methods to perform post-processing (i.e. quality control and normalization) as well as univariate statistical analysis of single and multi-omics data sets. These methods include quality control metrics, signal drift and batch effect correction, intensity transformation, univariate hypothesis testing, but also clustering (as well as annotation of metabolomics data). The data are handled in the standard Bioconductor formats (i.e. SummarizedExperiment and MultiAssayExperiment for single and multi-omics datasets, respectively; the alternative ExpressionSet and MultiDataSet formats are also supported for convenience). As a result, all methods can be readily chained as workflows. The pipeline can be further enriched by multivariate analysis and feature selection, by using the ropls and biosigner packages, which support the same formats. Data can be conveniently imported from and exported to text files. Although the methods were initially targeted to metabolomics data, most of the methods can be applied to other types of omics data (e.g., transcriptomics, proteomics).

This package contains all the datasets used in the PepsNMR package.

build graphs from pathway databases, render them by Rgraphviz.