Platform Design Info for The Manufacturer's Name Sugar_Cane.

Platform Design Info for The Manufacturer's Name Tomato.

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.

Platform Design Info for The Manufacturer's Name Bsubtilis.

PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.

Platform Design Info for The Manufacturer's Name HG_U95B.

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

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

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

ProteoMM is a statistical method to perform model-based peptide-level differential expression analysis of single or multiple datasets. For multiple datasets ProteoMM produces a single fold change and p-value for each protein across multiple datasets. ProteoMM provides functionality for normalization, missing value imputation and differential expression. Model-based peptide-level imputation and differential expression analysis component of package follows the analysis described in “A statistical framework for protein quantitation in bottom-up MS based proteomics" (Karpievitch et al. Bioinformatics 2009). EigenMS normalisation is implemented as described in "Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition." (Karpievitch et al. Bioinformatics 2009).

This package calculates probabilistic pathway scores using gene expression data. Gene expression values are aggregated into pathway-based scores using Bayesian network representations of biological pathways.

pairedGSEA makes it simple to run a paired Differential Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis. The package allows you to store intermediate results for further investiation, if desired. pairedGSEA comes with a wrapper function for running an Over-Representation Analysis (ORA) and functionalities for plotting the results.

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 Plasmodium_Anopheles.

Platform Design Info for The Manufacturer's Name HG_U95Av2.

This package provides a Bioconductor data package for the Varambally dataset.

This package provides a Bioconductor data package for the Grasso (2012) Prostate Cancer dataset.

Platform Design Info for The Manufacturer's Name NuGO_Hs1a520180.

Platform Design Info for The Manufacturer's Name AG.

Platform Design Info for The Manufacturer's Name HG-U133B.

Publicly available RNA-seq data is routinely used for retrospective analysis to elucidate new biology. Novel transcript discovery enabled by large collections of RNA-seq datasets has emerged as one of such analysis. To increase the power of transcript discovery from large collections of RNA-seq datasets, we developed a new R package named Pooling RNA-seq and Assembling Models (PRAM), which builds transcript models in intergenic regions from pooled RNA-seq datasets. This package includes functions for defining intergenic regions, extracting and pooling related RNA-seq alignments, predicting, selected, and evaluating transcript models.

Platform Design Info for The Manufacturer's Name RG_U34A.

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

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