This package performs tests for paired high-throughput data.

Platform Design Info for NimbleGen charm_hg18_example.

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

Platform Design Info for The Manufacturer's Name RAE230A.

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

This package provides functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.

Pviz adapts the Gviz package for protein sequences and data.

Platform Design Info for Affymetrix HuGene-1_1-st-v1.

Platform Design Info for The Manufacturer's Name U133_X3P.

Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes related to the candidate (e.g. Pathways or network neighbors).

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

Platform Design Info for NimbleGen hg18_60mer_expr.

Platform Design Info for The Manufacturer's Name HG-U133A_2.

Platform Design Info for The Manufacturer's Name S_aureus.

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

This package provides support for parallelized estimation of GLMs/GEEs, catering for dispersed data.

pathwayPCA is an integrative analysis tool that implements the principal component analysis (PCA) based pathway analysis approaches described in Chen et al. (2008), Chen et al. (2010), and Chen (2011). pathwayPCA allows users to: (1) Test pathway association with binary, continuous, or survival phenotypes. (2) Extract relevant genes in the pathways using the SuperPCA and AES-PCA approaches. (3) Compute principal components (PCs) based on the selected genes. These estimated latent variables represent pathway activities for individual subjects, which can then be used to perform integrative pathway analysis, such as multi-omics analysis. (4) Extract relevant genes that drive pathway significance as well as data corresponding to these relevant genes for additional in-depth analysis. (5) Perform analyses with enhanced computational efficiency with parallel computing and enhanced data safety with S4-class data objects. (6) Analyze studies with complex experimental designs, with multiple covariates, and with interaction effects, e.g., testing whether pathway association with clinical phenotype is different between male and female subjects. Citations: Chen et al. (2008) <https://doi.org/10.1093/bioinformatics/btn458>; Chen et al. (2010) <https://doi.org/10.1002/gepi.20532>; and Chen (2011) <https://doi.org/10.2202/1544-6115.1697>.

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

The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values.

Platform Design Info for The Manufacturer's Name DrosGenome1.

Mapping PSMs back to genome. The package builds SAM file from shotgun proteomics data The package also provides function to prepare annotation from GTF file.

Platform Design Info for The Manufacturer's Name HG_U95E.

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 Affymetrix CyRGene-1_0-st.