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.

Platform Design Info for The Manufacturer's Name MG_U74Av2.

Platform Design Info for Affymetrix miRNA-4_0.

This package provides a set of annotation maps describing the entire Gene Ontology assembled using data from PANTHER.

Platform Design Info for The Manufacturer's Name Citrus.

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).

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.

Platform Design Info for The Manufacturer's Name MG_U74C.

Platform Design Info for The Manufacturer's Name Tomato.

Platform Design Info for Affymetrix miRNA-3_1.

Significance assessment for distance measures of time-course protein profiles.

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

Platform Design Info for The Manufacturer's Name HG-U219.

Platform Design Info for The Manufacturer's Name ATH1-121501.

Platform Design Info for The Manufacturer's Name U133_X3P.

This package provide simulation based methods for evaluating the statistical power in differential expression analysis from RNA-seq data.

Platform Design Info for The Manufacturer's Name AG.

This package provides a fast, convenient tool to identify the TSSs of miRNAs by integrating the data of H3K4me3 and Pol II as well as combining the conservation level and sequence feature, provided within both command-line and graphical interfaces, which achieves a better performance than the previous non-cell-specific methods on miRNA TSSs.

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

Annotated HPLC-ESI-MS lipid data in positive ionization mode from an experiment in which cultures of the marine diatom Phaeodactylum tricornutum were treated with various concentrations of hydrogen peroxide (H2O2) to induce oxidative stress. The experiment is described in Graff van Creveld, et al., 2015, "Early perturbation in mitochondria redox homeostasis in response to environmental stress predicts cell fate in diatoms," ISME Journal 9:385-395. PtH2O2lipids consists of two objects: A CAMERA xsAnnotate object (ptH2O2lipids$xsAnnotate) and LOBSTAHS LOBSet object (ptH2O2lipids$xsAnnotate$LOBSet). The LOBSet includes putative compound assignments from the default LOBSTAHS database. Isomer annotation is recorded in three other LOBSet slots.

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

Platform Design Info for Affymetrix miRNA-2_0.

This package contains R functions to predict biological variables to from placnetal DNA methylation data generated from infinium arrays. This includes inferring ethnicity/ancestry, gestational age, and cell composition from placental DNA methylation array (450k/850k) data.

PhenoPath infers genomic trajectories (pseudotimes) in the presence of heterogeneous genetic and environmental backgrounds and tests for interactions between them.