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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.
This package provides an association test that is capable of dealing with very rare and even private variants. This is accomplished by a kernel-based approach that takes the positions of the variants into account. The test can be used for pre-processed matrix data, but also directly for variant data stored in VCF files. Association testing can be performed whole-genome, whole-exome, or restricted to pre-defined regions of interest. The test is complemented by tools for analyzing and visualizing the results.
This package is a gene/phenotype prioritization tool that utilizes multiplex heterogeneous gene phenotype network. PhenoGeneRanker allows multi-layer gene and phenotype networks. It also calculates empirical p-values of gene/phenotype ranking using random stratified sampling of genes/phenotypes based on their connectivity degree in the network. https://dl.acm.org/doi/10.1145/3307339.3342155.
Platform Design Info for The Manufacturer's Name Cotton.
Platform Design Info for The Manufacturer's Name U133_X3P.
Platform Design Info for The Manufacturer's Name Medicago.
Platform Design Info for Affymetrix GuiGene-1_0-st.
This is a package that includes pre-processing and quality control functions that can remove margin events, compensate and transform the data and that will use PeacoQCSignalStability for quality control. This last function will first detect peaks in each channel of the flowframe. It will remove anomalies based on the IsolationTree function and the MAD outlier detection method. This package can be used for both flow- and mass cytometry data.
It uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.
CNV detection tool for targeted NGS panel data. Extension of the cn.mops package.
Platform Design Info for Affymetrix OviGene-1_1-st.
Platform Design Info for The Manufacturer's Name Porcine.
Platform Design Info for The Manufacturer's Name Rat230_2.
Platform Design Info for Affymetrix Cytogenetics_Array.
Platform Design Info for The Manufacturer's Name Mu11KsubB.
Platform Design Info for Affymetrix CHOGene-2_1-st.
Platform Design Info for NimbleGen 2006-07-18_mm8_refseq_promoter.
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.
Platform Design Info for Affymetrix MoGene-2_0-st.
Platform Design Info for Affymetrix RJpGene-1_0-st.
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 DroGene-1_1-st.
The Parallel Mixed Model (PMM) approach is suitable for hit selection and cross-comparison of RNAi screens generated in experiments that are performed in parallel under several conditions. For example, we could think of the measurements or readouts from cells under RNAi knock-down, which are infected with several pathogens or which are grown from different cell lines.
This package provides a Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset.