This R package helps the user identify k-mers (e.g. di- or tri-nucleotides) present periodically in a set of genomic loci (typically regulatory elements). The functions of this package provide a straightforward approach to find periodic occurrences of k-mers in DNA sequences, such as regulatory elements. It is not aimed at identifying motifs separated by a conserved distance; for this type of analysis, please visit MEME website.

Store UCSC phyloP mm39 conservation scores AnnotationHub Resource Metadata. Provide provenance and citation information for UCSC phyloP mm39 conservation score AnnotationHub resources. Illustrate in a vignette how to access those resources.

Platform Design Info for The Manufacturer's Name E_coli_2.

PAA imports single color (protein) microarray data that has been saved in gpr file format - esp. ProtoArray data. After preprocessing (background correction, batch filtering, normalization) univariate feature preselection is performed (e.g., using the "minimum M statistic" approach - hereinafter referred to as "mMs"). Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Therefore, either a frequency-based backwards elimination aproach or ensemble feature selection can be used. PAA provides a complete toolbox of analysis tools including several different plots for results examination and evaluation.

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.

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.

Platform Design Info for The Manufacturer's Name HT_MG-430A.

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

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 HG_U95Av2.

Platform Design Info for The Manufacturer's Name Mouse430_2.

Platform Design Info for The Manufacturer's Name Medicago.

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

Platform Design Info for Affymetrix Clariom_D_Human.

Runs PANDA, an algorithm for discovering novel network structure by combining information from multiple complementary data sources.

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.

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

This package provides a package containing metadata for POCRC arrays assembled using data from public repositories.

Platform Design Info for The Manufacturer's Name HG_U95B.

Platform Design Info for The Manufacturer's Name Poplar.

Platform Design Info for The Manufacturer's Name Vitis_Vinifera.

Statistical analysis of peptide microarrays.

Platform Design Info for NimbleGen 2006-07-18_mm8_refseq_promoter.

Platform Design Info for The Manufacturer's Name wheat.