Platform Design Info for The Manufacturer's Name X_tropicalis.

Routines to handle family data with a Pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for Pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the Pedigree object with various criteria, and kinship for the X chromosome.

Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.

Platform Design Info for Affymetrix MoGene-2_0-st.

Two experimental datasets to illustrate running and analysing phylogenetic profiles with PhyloProfile package.

This package provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV.

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

This package provides a package for processing protein mass spectrometry data.

This package provides functions to Analyze Microarray (Gene Expression) Data.

This package contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.

PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs.

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

This package provides a tool that enables in silico identification, integration, and modeling of mRNA features that influence post-transcriptional regulation of gene expression at a transcriptome-wide scale.

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

Phantasus is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.

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

Platform Design Info for The Manufacturer's Name Hu6800.

Platform Design Info for The Manufacturer's Name RG_U34C.

Platform Design Info for The Manufacturer's Name HG_U95D.

This package provides a package containing an environment representing the Pae_G1a.CDF file.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Poplar\_probe\_tab.

PhIPData defines an S4 class for phage-immunoprecipitation sequencing (PhIP-seq) experiments. Buliding upon the RangedSummarizedExperiment class, PhIPData enables users to coordinate metadata with experimental data in analyses. Additionally, PhIPData provides specialized methods to subset and identify beads-only samples, subset objects using virus aliases, and use existing peptide libraries to populate object parameters.

This package provides a package containing an environment representing the Poplar.cdf file.

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