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PhosR is a package for the comprenhensive analysis of phosphoproteomic data. There are two major components to PhosR: processing and downstream analysis. PhosR consists of various processing tools for phosphoproteomics data including filtering, imputation, normalisation, and functional analysis for inferring active kinases and signalling pathways.
Platform Design Info for Affymetrix miRNA-3_0.
Platform Design Info for The Manufacturer's Name MG_U74A.
Platform Design Info for The Manufacturer's Name Rhesus.
The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.
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.
This package provides a tool that enables in silico identification, integration, and modeling of mRNA features that influence post-transcriptional regulation of gene expression at a transcriptome-wide scale.
Platform Design Info for The Manufacturer's Name HG-U219.
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.
Runs PANDA, an algorithm for discovering novel network structure by combining information from multiple complementary data sources.
Platform Design Info for The Manufacturer's Name Rice.
Platform Design Info for The Manufacturer's Name Bsubtilis.
Platform Design Info for Affymetrix MoGene-1_1-st-v1.
Platform Design Info for The Manufacturer's Name MG_U74Bv2.
Platform Design Info for Affymetrix miRNA-2_0.
Platform Design Info for Affymetrix CanGene-1_1-st.
The complexity of high-throughput quantitative omics experiments often leads to low replicates numbers and many missing values. We implemented a new test to simultaneously consider missing values and quantitative changes, which we combined with well-performing statistical tests for high confidence detection of differentially regulated features. The package contains functions to run the test and to visualize the results.
pathlinkR is an R package designed to facilitate analysis of RNA-Seq results. Specifically, our aim with pathlinkR was to provide a number of tools which take a list of DE genes and perform different analyses on them, aiding with the interpretation of results. Functions are included to perform pathway enrichment, with muliplte databases supported, and tools for visualizing these results. Genes can also be used to create and plot protein-protein interaction networks, all from inside of R.
Platform Design Info for The Manufacturer's Name HG_U95B.
Platform Design Info for NimbleGen 2006-07-18_mm8_refseq_promoter.
Pqsfinder detects DNA and RNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, pqsfinder is able to detect G4s folded from imperfect G-runs containing bulges or mismatches or G4s having long loops. Pqsfinder also assigns an integer score to each hit that was fitted on G4 sequencing data and corresponds to expected stability of the folded G4.
Platform Design Info for Affymetrix EquGene-1_1-st.
Platform Design Info for Affymetrix Clariom_S_Rat.
Platform Design Info for Affymetrix CHOGene-2_1-st.