Platform Design Info for The Manufacturer's Name Yeast_2.

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

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.

PhantasusLite – a lightweight package with helper functions of general interest extracted from phantasus package. In parituclar it simplifies working with public RNA-seq datasets from GEO by providing access to the remote HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects.

Platform Design Info for Affymetrix miRNA-2_0.

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

This is a simple data package including various data sets derived from the estrogen data for use with the puma (Propagating Uncertainty in Microarray Analysis) package.

This package contains the data employed in the vignette of the PathNet package. These data belong to the following publication: 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.

This package implements a general purpose gene set analysis method called PADOG that downplays the importance of genes that apear often accross the sets of genes to be analyzed. The package provides also a benchmark for gene set analysis methods in terms of sensitivity and ranking using 24 public datasets from KEGGdzPathwaysGEO package.

Platform Design Info for Affymetrix MoGene-2_1-st.

Platform Design Info for Affymetrix Mapping250K_Sty.

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

Platform Design Info for The Manufacturer's Name Medicago.

Platform Design Info for The Manufacturer's Name X_tropicalis.

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

Platform Design Info for The Manufacturer's Name Hu6800.

Platform Design Info for The Manufacturer's Name RG_U34B.

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 PrimeView\_probe\_tab.

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 NimbleGen feinberg_hg18_me_hx1.

The package ptairData contains two raw datasets from Proton-Transfer-Reaction Time-of-Flight mass spectrometer acquisitions (PTR-TOF-MS), in the HDF5 format. One from the exhaled air of two volunteer healthy individuals with three replicates, and one from the cell culture headspace from two mycobacteria species and one control (culture medium only) with two replicates. Those datasets are used in the examples and in the vignette of the ptairMS package (PTR-TOF-MS data pre-processing). There are also used to gererate the ptrSet in the ptairMS data : exhaledPtrset and mycobacteriaSet.

Operate on `GInteractions` objects as tabular data using `dplyr`-like verbs. The functions and methods in `plyinteractions` provide a grammatical approach to manipulate `GInteractions`, to facilitate their integration in genomic analysis workflows.

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

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