PathNet uses topological information present in pathways and differential expression levels of genes (obtained from microarray experiment) to identify pathways that are 1) significantly enriched and 2) associated with each other in the context of differential expression. The algorithm is described in: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J. Source Code for Biology and Medicine 2012 Sep 24;7(1):10.

The PIUMA package offers a tidy pipeline of Topological Data Analysis frameworks to identify and characterize communities in high and heterogeneous dimensional data.

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

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

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

Platform Design Info for The Manufacturer's Name X_laevis_2.

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

Platform Design Info for Affymetrix HuEx-1_0-st-v2.

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

Platform Design Info for Affymetrix Mapping250K_Sty.

Platform Design Info for The Manufacturer's Name MG_U74A.

Platform Design Info for The Manufacturer's Name MOE430B.

Platform Design Info for The Manufacturer's Name Canine_2.

Platform Design Info for The Manufacturer's Name Mouse430_2.

This package provides a general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as described in Pounds et. al. (2009) Bioinformatics 25: 2013-2019.

This is a supplemental data package for the plotgardener package. Includes example datasets used in plotgardener vignettes and example raw data files. For details on how to use these datasets, see the plotgardener package vignettes.

Platform Design Info for Affymetrix RTA-1_0.

This package provides methods and tools for (pre-)processing of metabolomics datasets (i.e. peak matrices), including filtering, normalisation, missing value imputation, scaling, and signal drift and batch effect correction methods. Filtering methods are based on: the fraction of missing values (across samples or features); Relative Standard Deviation (RSD) calculated from the Quality Control (QC) samples; the blank samples. Normalisation methods include Probabilistic Quotient Normalisation (PQN) and normalisation to total signal intensity. A unified user interface for several commonly used missing value imputation algorithms is also provided. Supported methods are: k-nearest neighbours (knn), random forests (rf), Bayesian PCA missing value estimator (bpca), mean or median value of the given feature and a constant small value. The generalised logarithm (glog) transformation algorithm is available to stabilise the variance across low and high intensity mass spectral features. Finally, this package provides an implementation of the Quality Control-Robust Spline Correction (QCRSC) algorithm for signal drift and batch effect correction of mass spectrometry-based datasets.

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.

Platform Design Info for The Manufacturer's Name Bsubtilis.

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

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

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

Statistical analysis of peptide microarrays.